label int64 0 1 | func1 stringlengths 173 53.1k | func2 stringlengths 173 53.1k | id int64 0 901k |
|---|---|---|---|
0 | public static String convertStringToMD5(String toEnc) { try { MessageDigest mdEnc = MessageDigest.getInstance("MD5"); mdEnc.update(toEnc.getBytes(), 0, toEnc.length()); return new BigInteger(1, mdEnc.digest()).toString(16); } catch (Exception e) { return null; } } | private static Properties load(URL url) { Properties props = new Properties(); try { InputStream is = null; try { is = url.openStream(); props.load(is); } finally { is.close(); } } catch (IOException e) { } return props; } | 885,700 |
1 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | 885,701 |
0 | public void setContentAsStream(final InputStream input) throws IOException { ByteArrayOutputStream output = new ByteArrayOutputStream(); try { IOUtils.copy(input, output); } finally { output.close(); } this.content = output.toByteArray(); } | public void testSimpleHttpPostsHTTP10() throws Exception { int reqNo = 20; Random rnd = new Random(); List testData = new ArrayList(reqNo); for (int i = 0; i < reqNo; i++) { int size = rnd.nextInt(5000); byte[] data = new byte[size]; rnd.nextBytes(data); testData.add(data); } this.server.registerHandler("*", new HttpRequestHandler() { public void handle(final HttpRequest request, final HttpResponse response, final HttpContext context) throws HttpException, IOException { if (request instanceof HttpEntityEnclosingRequest) { HttpEntity incoming = ((HttpEntityEnclosingRequest) request).getEntity(); byte[] data = EntityUtils.toByteArray(incoming); ByteArrayEntity outgoing = new ByteArrayEntity(data); outgoing.setChunked(false); response.setEntity(outgoing); } else { StringEntity outgoing = new StringEntity("No content"); response.setEntity(outgoing); } } }); this.server.start(); this.client.getParams().setParameter(CoreProtocolPNames.PROTOCOL_VERSION, HttpVersion.HTTP_1_0); DefaultHttpClientConnection conn = new DefaultHttpClientConnection(); HttpHost host = new HttpHost("localhost", this.server.getPort()); try { for (int r = 0; r < reqNo; r++) { if (!conn.isOpen()) { Socket socket = new Socket(host.getHostName(), host.getPort()); conn.bind(socket, this.client.getParams()); } BasicHttpEntityEnclosingRequest post = new BasicHttpEntityEnclosingRequest("POST", "/"); byte[] data = (byte[]) testData.get(r); ByteArrayEntity outgoing = new ByteArrayEntity(data); post.setEntity(outgoing); HttpResponse response = this.client.execute(post, host, conn); assertEquals(HttpVersion.HTTP_1_0, response.getStatusLine().getProtocolVersion()); byte[] received = EntityUtils.toByteArray(response.getEntity()); byte[] expected = (byte[]) testData.get(r); assertEquals(expected.length, received.length); for (int i = 0; i < expected.length; i++) { assertEquals(expected[i], received[i]); } if (!this.client.keepAlive(response)) { conn.close(); } } HttpConnectionMetrics cm = conn.getMetrics(); assertEquals(reqNo, cm.getRequestCount()); assertEquals(reqNo, cm.getResponseCount()); } finally { conn.close(); this.server.shutdown(); } } | 885,702 |
0 | private static void copyFile(File in, File out) throws IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); FileChannel outChannel = new FileOutputStream(out).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } } | private String protectMarkup(String content, String markupRegex, String replaceSource, String replaceTarget) { Matcher matcher = Pattern.compile(markupRegex, Pattern.MULTILINE | Pattern.DOTALL).matcher(content); StringBuffer result = new StringBuffer(); while (matcher.find()) { String protectedMarkup = matcher.group(); protectedMarkup = protectedMarkup.replaceAll(replaceSource, replaceTarget); try { MessageDigest digest = MessageDigest.getInstance("MD5"); digest.reset(); digest.update(protectedMarkup.getBytes("UTF-8")); String hash = bytesToHash(digest.digest()); matcher.appendReplacement(result, hash); c_protectionMap.put(hash, protectedMarkup); m_hashList.add(hash); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } catch (UnsupportedEncodingException e) { e.printStackTrace(); } } matcher.appendTail(result); return result.toString(); } | 885,703 |
0 | @NotNull public Set<Class<?>> in(Package pack) { String packageName = pack.getName(); String packageOnly = pack.getName(); final boolean recursive = true; Set<Class<?>> classes = new LinkedHashSet<Class<?>>(); String packageDirName = packageOnly.replace('.', '/'); Enumeration<URL> dirs; try { dirs = Thread.currentThread().getContextClassLoader().getResources(packageDirName); } catch (IOException e) { throw new PackageScanFailedException("Could not read from package directory: " + packageDirName, e); } while (dirs.hasMoreElements()) { URL url = dirs.nextElement(); String protocol = url.getProtocol(); if ("file".equals(protocol)) { try { findClassesInDirPackage(packageOnly, URLDecoder.decode(url.getFile(), "UTF-8"), recursive, classes); } catch (UnsupportedEncodingException e) { throw new PackageScanFailedException("Could not read from file: " + url, e); } } else if ("jar".equals(protocol)) { JarFile jar; try { jar = ((JarURLConnection) url.openConnection()).getJarFile(); } catch (IOException e) { throw new PackageScanFailedException("Could not read from jar url: " + url, e); } Enumeration<JarEntry> entries = jar.entries(); while (entries.hasMoreElements()) { JarEntry entry = entries.nextElement(); String name = entry.getName(); if (name.charAt(0) == '/') { name = name.substring(1); } if (name.startsWith(packageDirName)) { int idx = name.lastIndexOf('/'); if (idx != -1) { packageName = name.substring(0, idx).replace('/', '.'); } if ((idx != -1) || recursive) { if (name.endsWith(".class") && !entry.isDirectory()) { String className = name.substring(packageName.length() + 1, name.length() - 6); add(packageName, classes, className); } } } } } } return classes; } | public static int[] BubbleSortDEC(int[] values) { boolean change = true; int aux; int[] indexes = new int[values.length]; for (int i = 0; i < values.length; i++) { indexes[i] = i; } while (change) { change = false; for (int i = 0; i < values.length - 1; i++) { if (values[i] < values[i + 1]) { aux = values[i]; values[i] = values[i + 1]; values[i + 1] = aux; aux = indexes[i]; indexes[i] = indexes[i + 1]; indexes[i + 1] = aux; change = true; } } } return (indexes); } | 885,704 |
0 | public static String md5(String text) { MessageDigest msgDigest = null; try { msgDigest = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw new IllegalStateException("System doesn't support MD5 algorithm."); } try { msgDigest.update(text.getBytes(AlipayConfig.CharSet)); } catch (UnsupportedEncodingException e) { throw new IllegalStateException("System doesn't support your EncodingException."); } byte[] bytes = msgDigest.digest(); String md5Str = new String(encodeHex(bytes)); return md5Str; } | public static StringBuffer readURLText(URL url, StringBuffer errorText) { StringBuffer page = new StringBuffer(""); String thisLine; try { BufferedReader source = new BufferedReader(new InputStreamReader(url.openStream())); while ((thisLine = source.readLine()) != null) { page.append(thisLine + "\n"); } return page; } catch (Exception e) { return errorText; } } | 885,705 |
0 | private void addIngredients(Recipe recipe, int id) throws Exception { PreparedStatement pst = null; try { conn = getConnection(); pst = conn.prepareStatement("INSERT INTO ingredients (recipe_id, name, amount, measure_id, shop_flag) VALUES (?,?,?,?,?)"); IngredientContainer ings = recipe.getIngredients(); Ingredient ingBean = null; Iterator it; for (it = ings.getIngredients().iterator(); it.hasNext(); ) { ingBean = (Ingredient) it.next(); pst.setInt(1, id); pst.setString(2, ingBean.getName()); pst.setDouble(3, ingBean.getAmount()); pst.setInt(4, ingBean.getType()); pst.setInt(5, ingBean.getShopFlag()); pst.executeUpdate(); } conn.commit(); } catch (Exception e) { conn.rollback(); MainFrame.appendStatusText("Can't add ingredient, the exception was " + e.getMessage()); } finally { try { if (pst != null) pst.close(); pst = null; } catch (Exception ex) { MainFrame.appendStatusText("Can't close database connection."); } } } | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | 885,706 |
0 | @Test public void testXMLDBURLStreamHandler() { System.out.println("testXMLDBURLStreamHandler"); ByteArrayOutputStream baos = new ByteArrayOutputStream(); try { URL url = new URL(XMLDB_URL_1); InputStream is = url.openStream(); copyDocument(is, baos); is.close(); } catch (Exception ex) { ex.printStackTrace(); LOG.error(ex); fail(ex.getMessage()); } } | private static void fileUpload() throws Exception { DefaultHttpClient httpclient = new DefaultHttpClient(); HttpPost httppost = new HttpPost(postURL); file = new File("h:\\Fantastic face.jpg"); MultipartEntity mpEntity = new MultipartEntity(HttpMultipartMode.BROWSER_COMPATIBLE); ContentBody cbFile = new FileBody(file); mpEntity.addPart("MAX_FILE_SIZE", new StringBody("2147483647")); mpEntity.addPart("owner", new StringBody("")); mpEntity.addPart("pin", new StringBody(pin)); mpEntity.addPart("base", new StringBody(base)); mpEntity.addPart("host", new StringBody("letitbit.net")); mpEntity.addPart("file0", cbFile); httppost.setEntity(mpEntity); System.out.println("executing request " + httppost.getRequestLine()); System.out.println("Now uploading your file into letitbit.net"); HttpResponse response = httpclient.execute(httppost); HttpEntity resEntity = response.getEntity(); System.out.println(response.getStatusLine()); if (resEntity != null) { uploadresponse = EntityUtils.toString(resEntity); } System.out.println("Upload response : " + uploadresponse); } | 885,707 |
1 | public void actionPerformed(ActionEvent ev) { if (fileChooser == null) { fileChooser = new JFileChooser(); ExtensionFileFilter fileFilter = new ExtensionFileFilter("Device profile (*.jar, *.zip)"); fileFilter.addExtension("jar"); fileFilter.addExtension("zip"); fileChooser.setFileFilter(fileFilter); } if (fileChooser.showOpenDialog(SwingSelectDevicePanel.this) == JFileChooser.APPROVE_OPTION) { String manifestDeviceName = null; URL[] urls = new URL[1]; ArrayList descriptorEntries = new ArrayList(); JarFile jar = null; try { jar = new JarFile(fileChooser.getSelectedFile()); Manifest manifest = jar.getManifest(); if (manifest != null) { Attributes attrs = manifest.getMainAttributes(); manifestDeviceName = attrs.getValue("Device-Name"); } for (Enumeration en = jar.entries(); en.hasMoreElements(); ) { String entry = ((JarEntry) en.nextElement()).getName(); if ((entry.toLowerCase().endsWith(".xml") || entry.toLowerCase().endsWith("device.txt")) && !entry.toLowerCase().startsWith("meta-inf")) { descriptorEntries.add(entry); } } urls[0] = fileChooser.getSelectedFile().toURL(); } catch (IOException e) { Message.error("Error reading file: " + fileChooser.getSelectedFile().getName() + ", " + Message.getCauseMessage(e), e); return; } finally { if (jar != null) { try { jar.close(); } catch (IOException ignore) { } } } if (descriptorEntries.size() == 0) { Message.error("Cannot find any device profile in file: " + fileChooser.getSelectedFile().getName()); return; } if (descriptorEntries.size() > 1) { manifestDeviceName = null; } ClassLoader classLoader = Common.createExtensionsClassLoader(urls); HashMap devices = new HashMap(); for (Iterator it = descriptorEntries.iterator(); it.hasNext(); ) { String entryName = (String) it.next(); try { devices.put(entryName, DeviceImpl.create(emulatorContext, classLoader, entryName, J2SEDevice.class)); } catch (IOException e) { Message.error("Error parsing device profile, " + Message.getCauseMessage(e), e); return; } } for (Enumeration en = lsDevicesModel.elements(); en.hasMoreElements(); ) { DeviceEntry entry = (DeviceEntry) en.nextElement(); if (devices.containsKey(entry.getDescriptorLocation())) { devices.remove(entry.getDescriptorLocation()); } } if (devices.size() == 0) { Message.info("Device profile already added"); return; } try { File deviceFile = new File(Config.getConfigPath(), fileChooser.getSelectedFile().getName()); if (deviceFile.exists()) { deviceFile = File.createTempFile("device", ".jar", Config.getConfigPath()); } IOUtils.copyFile(fileChooser.getSelectedFile(), deviceFile); DeviceEntry entry = null; for (Iterator it = devices.keySet().iterator(); it.hasNext(); ) { String descriptorLocation = (String) it.next(); Device device = (Device) devices.get(descriptorLocation); if (manifestDeviceName != null) { entry = new DeviceEntry(manifestDeviceName, deviceFile.getName(), descriptorLocation, false); } else { entry = new DeviceEntry(device.getName(), deviceFile.getName(), descriptorLocation, false); } lsDevicesModel.addElement(entry); Config.addDeviceEntry(entry); } lsDevices.setSelectedValue(entry, true); } catch (IOException e) { Message.error("Error adding device profile, " + Message.getCauseMessage(e), e); return; } } } | public void run() { XmlFilesFilter filter = new XmlFilesFilter(); String pathTemp = Settings.get("vo_store.databaseMetaCollection"); String sectionName = pathTemp.substring(1, pathTemp.indexOf("/", 2)); String templateName = VOAccess.getElementByName(settingsDB, "TEMPLATE", sectionName); String schemaName = VOAccess.getElementByName(settingsDB, "SCHEMA", sectionName); byte[] buf = new byte[1024]; Hashtable templateElements = null; try { URL xmlTemplateUrl = new URL(httpURI + settingsDB + "/" + templateName); URL getDocPathsAndValuesXslUrl = new URL(httpURI + settingsDB + "/" + "getDocPathsValuesAndDisplays.xsl"); org.w3c.dom.Document curTemplateXml = VOAccess.readDocument(xmlTemplateUrl); DOMResult templateResult = new DOMResult(); InputStream tempInput = getDocPathsAndValuesXslUrl.openStream(); javax.xml.transform.sax.SAXSource tempXslSource = new javax.xml.transform.sax.SAXSource(new org.xml.sax.InputSource(tempInput)); Transformer trans = TransformerFactory.newInstance().newTransformer(tempXslSource); trans.setParameter("schemaUrl", httpURI + settingsDB + "/" + schemaName); trans.transform(new javax.xml.transform.dom.DOMSource(curTemplateXml), templateResult); tempInput.close(); templateElements = VOAccess.displaysToHashtable(templateResult); ((CollectionManagementService) CollectionsManager.getService(xmldbURI + rootDB, false, "CollectionManager")).createCollection(rootDB + pathTemp); } catch (Exception ex) { logger.error("Error parsing input document", ex); ex.printStackTrace(); } while (true) { File[] fileList = sourceMetaFilesDir.listFiles(filter); for (int i = 0; i < Math.min(fileList.length, 500); i++) { File newFile = fileList[i]; try { Document metaDoc = build.build(newFile); Element metaElm = metaDoc.getRootElement(); String dataFileName = metaElm.getChildText("Content"), previewFileName = metaElm.getChildText("Preview"); String objId = VOAccess.getUniqueId(); metaElm.getChild("Content").setText("videostore?type=doc&objId=" + objId); metaElm.getChild("Preview").setText("videostore?type=preview&objId=" + objId); boolean found = false; for (Iterator it = sourceDataFilesDirs.iterator(); it.hasNext() && !found; ) { String sourceDataFilesDir = (String) it.next(); File dataInput = new File(sourceDataFilesDir + "/" + dataFileName); if (dataInput.exists()) { found = true; BufferedInputStream inp = new BufferedInputStream(new FileInputStream(dataInput)); FileOutputStream outp = new FileOutputStream(new File(targetDataFilesDirs.get(curDirWriteTo) + "/" + objId + ".dat")); int read = inp.read(buf, 0, buf.length); while (read > 0) { outp.write(buf, 0, read); read = inp.read(buf, 0, buf.length); } inp.close(); outp.flush(); outp.close(); dataInput = new File(sourceDataFilesDir + "/" + previewFileName); inp = new BufferedInputStream(new FileInputStream(dataInput)); outp = new FileOutputStream(new File(targetDataFilesDirs.get(curDirWriteTo) + "/" + objId + ".jpg")); read = inp.read(buf, 0, buf.length); while (read > 0) { outp.write(buf, 0, read); read = inp.read(buf, 0, buf.length); } inp.close(); outp.flush(); outp.close(); curDirWriteTo++; if (curDirWriteTo >= targetDataFilesDirs.size()) { curDirWriteTo = 0; } } } if (!found) { newFile.renameTo(new File(newFile.getAbsolutePath() + ".not_found")); } else { String title = getValueByPath((String) templateElements.get("title"), metaDoc.getRootElement()); String description = getValueByPath((String) templateElements.get("description"), metaDoc.getRootElement()); String onlink = ""; if (null != templateElements.get("onlink")) { onlink = getValueByPath((String) templateElements.get("onlink"), metaDoc.getRootElement()); } String ncover = ""; if (null != templateElements.get("ncover")) { ncover = getValueByPath((String) templateElements.get("ncover"), metaDoc.getRootElement()); } String wcover = ""; if (null != templateElements.get("wcover")) { wcover = getValueByPath((String) templateElements.get("wcover"), metaDoc.getRootElement()); } String ecover = ""; if (null != templateElements.get("ecover")) { ecover = getValueByPath((String) templateElements.get("ecover"), metaDoc.getRootElement()); } String scover = ""; if (null != templateElements.get("scover")) { scover = getValueByPath((String) templateElements.get("scover"), metaDoc.getRootElement()); } String datefrom = ""; if (null != templateElements.get("datefrom")) { datefrom = getValueByPath((String) templateElements.get("datefrom"), metaDoc.getRootElement()); } String dateto = ""; if (null != templateElements.get("dateto")) { dateto = getValueByPath((String) templateElements.get("dateto"), metaDoc.getRootElement()); } String previewimg = ""; if (null != templateElements.get("previewimg")) { previewimg = getValueByPath((String) templateElements.get("previewimg"), metaDoc.getRootElement()); } String discRestr = "false"; String votingRestr = "false"; datefrom = VOAccess.parseDate(datefrom, "yyyy-MM-dd'T'HH:mm:ss", VO.defaultTimeFormat.toPattern()); dateto = VOAccess.parseDate(datefrom, "yyyy-MM-dd'T'HH:mm:ss", VO.defaultTimeFormat.toPattern()); Hashtable discussionFields = new Hashtable(); discussionFields.put("OBJECT_ID", objId); discussionFields.put("AUTHOR_ID", "auto"); discussionFields.put("AUTHOR_NAME", "auto"); discussionFields.put("OBJECT_SECTION", sectionName); discussionFields.put("OBJECT_PATH", pathTemp); discussionFields.put("FILE_PATH", ""); discussionFields.put("TITLE", title); discussionFields.put("DESCRIPTION", description); discussionFields.put("ONLINK", onlink); discussionFields.put("NCOVER", ncover); discussionFields.put("ECOVER", ecover); discussionFields.put("SCOVER", scover); discussionFields.put("WCOVER", wcover); discussionFields.put("PERIOD_START", datefrom); discussionFields.put("PERIOD_END", dateto); discussionFields.put("PREVIEW_IMG", previewimg); discussionFields.put("DISCUSSRESTRICTION", discRestr); discussionFields.put("VOTINGRESTRICTION", votingRestr); VOAccess.createDiscussionFile(discussionFields); VOAccess.updateLastItem(objId, sectionName); Collection col = CollectionsManager.getCollection(rootDB + pathTemp, true); XMLResource document = (XMLResource) col.createResource(objId + ".xml", XMLResource.RESOURCE_TYPE); document.setContent(outXml.outputString(metaElm)); col.storeResource(document); Indexer.index(objId); newFile.delete(); } } catch (Exception ex) { logger.error("Error parsing input document", ex); ex.printStackTrace(); newFile.renameTo(new File(newFile.getAbsolutePath() + ".bad")); } } try { this.sleep(600000); } catch (InterruptedException ex1) { ex1.printStackTrace(); } } } | 885,708 |
0 | public void copyFile(String source_name, String dest_name) throws IOException { File source_file = new File(source_name); File destination_file = new File(dest_name); FileInputStream source = null; FileOutputStream destination = null; byte[] buffer; int bytes_read; try { if (!source_file.exists() || !source_file.isFile()) throw new FileCopyException(QZ.PHRASES.getPhrase("25") + " " + source_name); if (!source_file.canRead()) throw new FileCopyException(QZ.PHRASES.getPhrase("26") + " " + QZ.PHRASES.getPhrase("27") + ": " + source_name); if (destination_file.exists()) { if (destination_file.isFile()) { DataInputStream in = new DataInputStream(System.in); String response; if (!destination_file.canWrite()) throw new FileCopyException(QZ.PHRASES.getPhrase("28") + " " + QZ.PHRASES.getPhrase("29") + ": " + dest_name); System.out.print(QZ.PHRASES.getPhrase("19") + dest_name + QZ.PHRASES.getPhrase("30") + ": "); System.out.flush(); response = in.readLine(); if (!response.equals("Y") && !response.equals("y")) throw new FileCopyException(QZ.PHRASES.getPhrase("31")); } else throw new FileCopyException(QZ.PHRASES.getPhrase("28") + " " + QZ.PHRASES.getPhrase("32") + ": " + dest_name); } else { File parentdir = parent(destination_file); if (!parentdir.exists()) throw new FileCopyException(QZ.PHRASES.getPhrase("28") + " " + QZ.PHRASES.getPhrase("33") + ": " + dest_name); if (!parentdir.canWrite()) throw new FileCopyException(QZ.PHRASES.getPhrase("28") + " " + QZ.PHRASES.getPhrase("34") + ": " + dest_name); } source = new FileInputStream(source_file); destination = new FileOutputStream(destination_file); buffer = new byte[1024]; while (true) { bytes_read = source.read(buffer); if (bytes_read == -1) break; destination.write(buffer, 0, bytes_read); } } finally { if (source != null) try { source.close(); } catch (IOException e) { ; } if (destination != null) try { destination.close(); } catch (IOException e) { ; } } } | private static URL handleRedirectUrl(URL url) { try { URLConnection cn = url.openConnection(); Utils.setHeader(cn); if (!(cn instanceof HttpURLConnection)) { return url; } HttpURLConnection hcn = (HttpURLConnection) cn; hcn.setInstanceFollowRedirects(false); int resCode = hcn.getResponseCode(); if (resCode == 200) { System.out.println("URL: " + url); return url; } String location = hcn.getHeaderField("Location"); hcn.disconnect(); return handleRedirectUrl(new URL(location.replace(" ", "%20"))); } catch (IOException e) { e.printStackTrace(); } return url; } | 885,709 |
0 | private void trySend(Primitive p) throws IOException { ByteArrayOutputStream out = new ByteArrayOutputStream(); try { mSerializer.serialize(p, out); } catch (SerializerException e) { mTxManager.notifyErrorResponse(p.getTransactionID(), ImErrorInfo.SERIALIZER_ERROR, "Internal serializer error, primitive: " + p.getType()); out.close(); return; } HttpPost req = new HttpPost(mPostUri); req.addHeader(mContentTypeHeader); if (mMsisdnHeader != null) { req.addHeader(mMsisdnHeader); } ByteArrayEntity entity = new ByteArrayEntity(out.toByteArray()); req.setEntity(entity); mLastActive = SystemClock.elapsedRealtime(); if (Log.isLoggable(ImpsLog.TAG, Log.DEBUG)) { long sendBytes = entity.getContentLength() + 176; ImpsLog.log(mConnection.getLoginUserName() + " >> " + p.getType() + " HTTP payload approx. " + sendBytes + " bytes"); } if (Log.isLoggable(ImpsLog.PACKET_TAG, Log.DEBUG)) { ImpsLog.dumpRawPacket(out.toByteArray()); ImpsLog.dumpPrimitive(p); } HttpResponse res = mHttpClient.execute(req); StatusLine statusLine = res.getStatusLine(); HttpEntity resEntity = res.getEntity(); InputStream in = resEntity.getContent(); if (Log.isLoggable(ImpsLog.PACKET_TAG, Log.DEBUG)) { Log.d(ImpsLog.PACKET_TAG, statusLine.toString()); Header[] headers = res.getAllHeaders(); for (Header h : headers) { Log.d(ImpsLog.PACKET_TAG, h.toString()); } int len = (int) resEntity.getContentLength(); if (len > 0) { byte[] content = new byte[len]; int offset = 0; int bytesRead = 0; do { bytesRead = in.read(content, offset, len); offset += bytesRead; len -= bytesRead; } while (bytesRead > 0); in.close(); ImpsLog.dumpRawPacket(content); in = new ByteArrayInputStream(content); } } try { if (statusLine.getStatusCode() != HttpURLConnection.HTTP_OK) { mTxManager.notifyErrorResponse(p.getTransactionID(), statusLine.getStatusCode(), statusLine.getReasonPhrase()); return; } if (resEntity.getContentLength() == 0) { if ((p.getTransactionMode() != TransactionMode.Response) && !p.getType().equals(ImpsTags.Polling_Request)) { mTxManager.notifyErrorResponse(p.getTransactionID(), ImErrorInfo.ILLEGAL_SERVER_RESPONSE, "bad response from server"); } return; } Primitive response = mParser.parse(in); if (Log.isLoggable(ImpsLog.PACKET_TAG, Log.DEBUG)) { ImpsLog.dumpPrimitive(response); } if (Log.isLoggable(ImpsLog.TAG, Log.DEBUG)) { long len = 2 + resEntity.getContentLength() + statusLine.toString().length() + 2; Header[] headers = res.getAllHeaders(); for (Header header : headers) { len += header.getName().length() + header.getValue().length() + 4; } ImpsLog.log(mConnection.getLoginUserName() + " << " + response.getType() + " HTTP payload approx. " + len + "bytes"); } if (!mReceiveQueue.offer(response)) { mTxManager.notifyErrorResponse(p.getTransactionID(), ImErrorInfo.UNKNOWN_ERROR, "receiving queue full"); } } catch (ParserException e) { ImpsLog.logError(e); mTxManager.notifyErrorResponse(p.getTransactionID(), ImErrorInfo.PARSER_ERROR, "Parser error, received a bad response from server"); } finally { resEntity.consumeContent(); } } | public static String getHashedPassword(String password) { try { MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(password.getBytes()); BigInteger hashedInt = new BigInteger(1, digest.digest()); return String.format("%1$032X", hashedInt); } catch (NoSuchAlgorithmException nsae) { System.err.println(nsae.getMessage()); } return ""; } | 885,710 |
0 | protected void initializeFromURL(URL url) throws IOException { URLConnection connection = url.openConnection(); String message = this.validateURLConnection(connection, DBASE_CONTENT_TYPES); if (message != null) { throw new IOException(message); } this.channel = Channels.newChannel(WWIO.getBufferedInputStream(connection.getInputStream())); this.initialize(); } | private void removeCollection(long oid, Connection conn) throws XMLDBException { try { String sql = "DELETE FROM X_DOCUMENT WHERE X_DOCUMENT.XDB_COLLECTION_OID = ?"; PreparedStatement pstmt = conn.prepareStatement(sql); pstmt.setLong(1, oid); pstmt.executeUpdate(); pstmt.close(); sql = "DELETE FROM XDB_COLLECTION WHERE XDB_COLLECTION.XDB_COLLECTION_OID = ?"; pstmt = conn.prepareStatement(sql); pstmt.setLong(1, oid); pstmt.executeUpdate(); pstmt.close(); removeChildCollection(oid, conn); } catch (java.sql.SQLException se) { try { conn.rollback(); } catch (java.sql.SQLException se2) { se2.printStackTrace(); } se.printStackTrace(); } } | 885,711 |
0 | private boolean adjust(String stationUrl) throws LastFMError { try { URL url = new URL("http://" + mBaseURL + "/adjust.php?session=" + mSession + "&url=" + URLEncoder.encode(stationUrl, "UTF-8")); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); conn.connect(); InputStream is = conn.getInputStream(); InputStreamReader reader = new InputStreamReader(is); BufferedReader stringReader = new BufferedReader(reader); Utils.OptionsParser options = new Utils.OptionsParser(stringReader); if (!options.parse()) options = null; stringReader.close(); if ("OK".equals(options.get("response"))) { return true; } else { Log.e(TAG, "Adjust failed: \"" + options.get("response") + "\""); return false; } } catch (MalformedURLException e) { Log.e(TAG, "in adjust", e); throw new LastFMError("Adjust failed:" + e.toString()); } catch (UnsupportedEncodingException e) { Log.e(TAG, "in adjust", e); throw new LastFMError("Adjust failed:" + e.toString()); } catch (IOException e) { Log.e(TAG, "in adjust", e); throw new LastFMError("Station not found:" + stationUrl); } } | private static byte[] tryLoadFile(String path) throws IOException { InputStream in = new FileInputStream(path); ByteArrayOutputStream out = new ByteArrayOutputStream(); IOUtils.copy(in, out); in.close(); out.close(); return out.toByteArray(); } | 885,712 |
1 | public static String md(String passwd) { MessageDigest md5 = null; String digest = passwd; try { md5 = MessageDigest.getInstance("MD5"); md5.update(passwd.getBytes()); byte[] digestData = md5.digest(); digest = byteArrayToHex(digestData); } catch (NoSuchAlgorithmException e) { LOG.warn("MD5 not supported. Using plain string as password!"); } catch (Exception e) { LOG.warn("Digest creation failed. Using plain string as password!"); } return digest; } | public static String md5(String value) throws NoSuchAlgorithmException { MessageDigest messageDigest = MessageDigest.getInstance("MD5"); try { messageDigest.update(value.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { messageDigest.update(value.getBytes()); } byte[] bytes = messageDigest.digest(); return byteArrayToHexString(bytes); } | 885,713 |
1 | private boolean copy(File in, File out) { try { FileInputStream fis = new FileInputStream(in); FileOutputStream fos = new FileOutputStream(out); FileChannel readableChannel = fis.getChannel(); FileChannel writableChannel = fos.getChannel(); writableChannel.truncate(0); writableChannel.transferFrom(readableChannel, 0, readableChannel.size()); fis.close(); fos.close(); return true; } catch (IOException ioe) { System.out.println("Copy Error: IOException during copy\r\n" + ioe.getMessage()); return false; } } | public void render(HttpServletRequest request, HttpServletResponse response, File file, final Throwable t, final String contentType, final String encoding) throws Exception { if (contentType != null) { response.setContentType(contentType); } if (encoding != null) { response.setCharacterEncoding(encoding); } if (file.length() > Integer.MAX_VALUE) { throw new IllegalArgumentException("Cannot send file greater than 2GB"); } response.setContentLength((int) file.length()); IOUtils.copy(new FileInputStream(file), response.getOutputStream()); } | 885,714 |
0 | @Override public EntrySet read(EntrySet set) throws ReadFailedException { if (!SourceCache.contains(url)) { SSL.certify(url); try { super.setParser(Parser.detectParser(url.openStream(), url)); final PipedInputStream in = new PipedInputStream(); final PipedOutputStream forParser = new PipedOutputStream(in); new Thread(new Runnable() { public void run() { try { OutputStream out = SourceCache.startCaching(url); InputStream is = url.openStream(); byte[] buffer = new byte[100000]; while (true) { int amountRead = is.read(buffer); if (amountRead == -1) { break; } forParser.write(buffer, 0, amountRead); out.write(buffer, 0, amountRead); } forParser.close(); out.close(); SourceCache.finish(url); } catch (IOException e) { e.printStackTrace(); } } }).start(); super.setIos(in); } catch (Exception e) { throw new ReadFailedException(e); } return super.read(set); } else { try { return SourceCache.get(url).read(set); } catch (IOException e) { throw new ReadFailedException(e); } } } | public static String getHash(String input) { MessageDigest m; try { m = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); return null; } m.update(input.getBytes(), 0, input.length()); return new BigInteger(1, m.digest()).toString(16); } | 885,715 |
1 | private static void processFile(StreamDriver driver, String sourceName) throws Exception { String destName = sourceName + ".xml"; File dest = new File(destName); if (dest.exists()) { throw new IllegalArgumentException("File '" + destName + "' already exists!"); } FileChannel sourceChannel = new FileInputStream(sourceName).getChannel(); try { MappedByteBuffer sourceByteBuffer = sourceChannel.map(FileChannel.MapMode.READ_ONLY, 0, sourceChannel.size()); CharsetDecoder decoder = Charset.forName("ISO-8859-15").newDecoder(); CharBuffer sourceBuffer = decoder.decode(sourceByteBuffer); driver.generateXmlDocument(sourceBuffer, new FileOutputStream(dest)); } finally { sourceChannel.close(); } } | private void copy(final File src, final File dstDir) { dstDir.mkdirs(); final File dst = new File(dstDir, src.getName()); BufferedReader reader = null; BufferedWriter writer = null; try { reader = new BufferedReader(new InputStreamReader(new FileInputStream(src), "ISO-8859-1")); writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(dst), "ISO-8859-1")); String read; while ((read = reader.readLine()) != null) { Line line = new Line(read); if (line.isComment()) continue; writer.write(read); writer.newLine(); } } catch (IOException e) { e.printStackTrace(); } finally { if (reader != null) try { reader.close(); } catch (IOException e) { } if (writer != null) { try { writer.flush(); } catch (IOException e) { } try { writer.close(); } catch (IOException e) { } } } } | 885,716 |
1 | public void gzipCompress(String file) { try { File inputFile = new File(file); FileInputStream fileinput = new FileInputStream(inputFile); File outputFile = new File(file.substring(0, file.length() - 1) + "z"); FileOutputStream stream = new FileOutputStream(outputFile); GZIPOutputStream gzipstream = new GZIPOutputStream(stream); BufferedInputStream bis = new BufferedInputStream(fileinput); int bytes_read = 0; byte[] buf = new byte[READ_BUFFER_SIZE]; while ((bytes_read = bis.read(buf, 0, BLOCK_SIZE)) != -1) { gzipstream.write(buf, 0, bytes_read); } bis.close(); inputFile.delete(); gzipstream.finish(); gzipstream.close(); } catch (FileNotFoundException fnfe) { System.out.println("Compressor: Cannot find file " + fnfe.getMessage()); } catch (SecurityException se) { System.out.println("Problem saving file " + se.getMessage()); } catch (IOException ioe) { System.out.println("Problem saving file " + ioe.getMessage()); } } | public static void main(String[] args) throws IOException, WrongFormatException, URISyntaxException { System.out.println(new URI("google.com.ua.css").toString()); Scanner scc = new Scanner(System.in); System.err.print(scc.nextLine().substring(1)); ServerSocket s = new ServerSocket(5354); while (true) { Socket client = s.accept(); InputStream iStream = client.getInputStream(); BufferedReader bf = new BufferedReader(new InputStreamReader(iStream)); String line = ""; while (!(line = bf.readLine()).equals("")) { System.out.println(line); } System.out.println("end of request"); new PrintWriter(client.getOutputStream()).println("hi"); bf.close(); } } | 885,717 |
0 | public void setRandom(boolean random) { this.random = random; if (random) { possibleScores = new int[NUM_SCORES]; for (int i = 0; i < NUM_SCORES - 1; i++) { getRandomScore: while (true) { int score = (int) (Math.random() * 20) + 1; for (int j = 0; j < i; j++) { if (score == possibleScores[j]) { continue getRandomScore; } } possibleScores[i] = score; break; } } possibleScores[NUM_SCORES - 1] = 25; boolean sorted = false; while (!sorted) { sorted = true; for (int i = 0; i < NUM_SCORES - 1; i++) { if (possibleScores[i] > possibleScores[i + 1]) { int t = possibleScores[i]; possibleScores[i] = possibleScores[i + 1]; possibleScores[i + 1] = t; sorted = false; } } } setPossibleScores(possibleScores); } } | public void login() { loginsuccessful = false; try { cookies = new StringBuilder(); HttpParams params = new BasicHttpParams(); params.setParameter("http.useragent", "Mozilla/5.0 (Windows; U; Windows NT 6.1; en-GB; rv:1.9.2) Gecko/20100115 Firefox/3.6"); DefaultHttpClient httpclient = new DefaultHttpClient(params); NULogger.getLogger().info("Trying to log in to crocko.com"); HttpPost httppost = new HttpPost("https://www.crocko.com/accounts/login"); List<NameValuePair> formparams = new ArrayList<NameValuePair>(); formparams.add(new BasicNameValuePair("login", getUsername())); formparams.add(new BasicNameValuePair("password", getPassword())); UrlEncodedFormEntity entity = new UrlEncodedFormEntity(formparams, "UTF-8"); httppost.setEntity(entity); HttpResponse httpresponse = httpclient.execute(httppost); NULogger.getLogger().info("Getting cookies........"); NULogger.getLogger().info(EntityUtils.toString(httpresponse.getEntity())); Iterator<Cookie> it = httpclient.getCookieStore().getCookies().iterator(); Cookie escookie = null; while (it.hasNext()) { escookie = it.next(); cookies.append(escookie.getName()).append("=").append(escookie.getValue()).append(";"); if (escookie.getName().equals("PHPSESSID")) { sessionid = escookie.getValue(); NULogger.getLogger().info(sessionid); } } if (cookies.toString().contains("logacc")) { NULogger.getLogger().info(cookies.toString()); loginsuccessful = true; username = getUsername(); password = getPassword(); NULogger.getLogger().info("Crocko login successful :)"); } if (!loginsuccessful) { NULogger.getLogger().info("Crocko.com Login failed :("); loginsuccessful = false; username = ""; password = ""; JOptionPane.showMessageDialog(NeembuuUploader.getInstance(), "<html><b>" + HOSTNAME + "</b> " + TranslationProvider.get("neembuuuploader.accounts.loginerror") + "</html>", HOSTNAME, JOptionPane.WARNING_MESSAGE); AccountsManager.getInstance().setVisible(true); } httpclient.getConnectionManager().shutdown(); } catch (Exception e) { NULogger.getLogger().log(Level.SEVERE, "{0}: {1}", new Object[] { getClass().getName(), e.toString() }); System.err.println(e); } } | 885,718 |
1 | public byte process(ProcessorContext<PublishRequest> context) throws InterruptedException, ProcessorException { logger.info("MapTileChacheTask:process"); PublishRequest req = context.getItem().getEntity(); if (StringUtils.isEmpty(req.getBackMap())) return TaskState.STATE_TILE_CACHED; final PublicMapPost post; final GenericDAO<PublicMapPost> postDao = DAOFactory.createDAO(PublicMapPost.class); try { ReadOnlyTransaction.beginTransaction(); } catch (DatabaseException e) { logger.error("error", e); throw new ProcessorException(e); } int numCachedTiles = 0; try { List<MapTile> backTiles = new ArrayList<MapTile>(); post = postDao.findUniqueByCriteria(Expression.eq("guid", req.getPostGuid())); final LatLngRectangle bounds = new LatLngRectangle(new LatLngPoint(post.getSWLat(), post.getSWLon()), new LatLngPoint(post.getNELat(), post.getNELon())); final String backMapGuid = "gst"; final XFile dstDir = new XFile(new XFile(Configuration.getInstance().getPublicMapStorage().toString()), backMapGuid); dstDir.mkdir(); for (int z = Math.min(Tile.getOptimalZoom(bounds, 768), 9); z <= 17; z++) { final Tile tileStart = new Tile(bounds.getSouthWest().getLat(), bounds.getSouthWest().getLng(), z); final Tile tileEnd = new Tile(bounds.getNorthEast().getLat(), bounds.getNorthEast().getLng(), z); for (double y = tileEnd.getTileCoord().getY(); y <= tileStart.getTileCoord().getY(); y++) for (double x = tileStart.getTileCoord().getX(); x <= tileEnd.getTileCoord().getX(); x++) { NASAMapTile tile = new NASAMapTile((int) x, (int) y, z); XFile file = new XFile(dstDir, tile.toKeyString()); if (file.exists() && file.isFile()) continue; backTiles.add(tile); } } try { for (MapTile tile : backTiles) { InputStream in = null; OutputStream out = null; final URL url = new URL(tile.getPath()); try { final XFile outFile = new XFile(dstDir, tile.toKeyString()); final URLConnection conn = url.openConnection(); if (conn == null || !conn.getContentType().startsWith("image")) throw new IllegalAccessException("onearth.jpl.nasa.gov service returns non-image file, " + "content-type='" + conn.getContentType() + "'"); in = conn.getInputStream(); if (in != null) { out = new XFileOutputStream(outFile); IOUtils.copy(in, out); } else throw new IllegalStateException("opened stream is null"); } finally { if (out != null) { out.flush(); out.close(); } if (in != null) in.close(); } if (++numCachedTiles % 100 == 0) { logger.info(numCachedTiles + " tiles cached"); } } } catch (Throwable e) { logger.error("map tile caching has failed: ", e); throw new ProcessorException(e); } } catch (ProcessorException e) { logger.error("map tile caching has failed: ", e); throw e; } catch (Throwable e) { logger.error("map tile caching has failed: ", e); throw new ProcessorException(e); } finally { ReadOnlyTransaction.closeTransaction(); logger.info(numCachedTiles + " tiles cached"); } return TaskState.STATE_TILE_CACHED; } | public static void copy(String sourceFile, String targetFile) throws IOException { FileChannel sourceChannel = new FileInputStream(sourceFile).getChannel(); FileChannel targetChannel = new FileOutputStream(targetFile).getChannel(); targetChannel.transferFrom(sourceChannel, 0, sourceChannel.size()); sourceChannel.close(); targetChannel.close(); } | 885,719 |
0 | private static StringBuffer downloadHTTPPage(URL url) throws Exception { URLConnection con = url.openConnection(); con.setReadTimeout(0); StringBuffer sb = new StringBuffer(); BufferedReader br = new BufferedReader(new InputStreamReader(con.getInputStream())); String line = null; while (null != (line = br.readLine())) { sb.append(line); } br.close(); return sb; } | @Test public void testCascadeTraining() throws IOException { File temp = File.createTempFile("fannj_", ".tmp"); temp.deleteOnExit(); IOUtils.copy(this.getClass().getResourceAsStream("parity8.train"), new FileOutputStream(temp)); Fann fann = new FannShortcut(8, 1); Trainer trainer = new Trainer(fann); float desiredError = .00f; float mse = trainer.cascadeTrain(temp.getPath(), 30, 1, desiredError); assertTrue("" + mse, mse <= desiredError); } | 885,720 |
1 | public void setTableBraille(String tableBraille, boolean sys) { fiConf.setProperty(OptNames.fi_braille_table, tableBraille); fiConf.setProperty(OptNames.fi_is_sys_braille_table, Boolean.toString(sys)); FileChannel in = null; FileChannel out = null; try { String fichTable; if (!(tableBraille.endsWith(".ent"))) { tableBraille = tableBraille + ".ent"; } if (sys) { fichTable = ConfigNat.getInstallFolder() + "xsl/tablesBraille/" + tableBraille; } else { fichTable = ConfigNat.getUserBrailleTableFolder() + tableBraille; } in = new FileInputStream(fichTable).getChannel(); out = new FileOutputStream(getUserBrailleTableFolder() + "Brltab.ent").getChannel(); in.transferTo(0, in.size(), out); in.close(); out.close(); } catch (IOException e) { e.printStackTrace(); } try { String fichTable; if (sys) { fichTable = ConfigNat.getInstallFolder() + "/xsl/tablesEmbosseuse/" + tableBraille; } else { fichTable = ConfigNat.getUserEmbossTableFolder() + "/" + tableBraille; } in = new FileInputStream(fichTable).getChannel(); out = new FileOutputStream(ConfigNat.getUserTempFolder() + "Table_pour_chaines.ent").getChannel(); in.transferTo(0, in.size(), out); in.close(); out.close(); } catch (IOException e) { e.printStackTrace(); } } | public static void copy(File file1, File file2) throws IOException { FileReader in = new FileReader(file1); FileWriter out = new FileWriter(file2); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } | 885,721 |
0 | public static byte[] getHashedPassword(String password, byte[] randomBytes) { byte[] hashedPassword = null; try { MessageDigest messageDigest = MessageDigest.getInstance("MD5"); messageDigest.update(randomBytes); messageDigest.update(password.getBytes("UTF-8")); hashedPassword = messageDigest.digest(); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } catch (UnsupportedEncodingException e) { e.printStackTrace(); } return hashedPassword; } | public void callUpdate() { LOGGER.debug("Checking for Updates"); new Thread() { @Override public void run() { String lastVersion = null; try { URL projectSite = new URL("http://code.google.com/p/g15lastfm/"); URLConnection urlC = projectSite.openConnection(); BufferedReader in = new BufferedReader(new InputStreamReader(urlC.getInputStream())); String inputLine; while ((inputLine = in.readLine()) != null) { if (inputLine.contains("<strong>Current version:")) { lastVersion = inputLine; break; } } in.close(); if (lastVersion != null && lastVersion.length() > 0) { lastVersion = lastVersion.substring(lastVersion.indexOf("Current version:") + 16); lastVersion = lastVersion.substring(0, lastVersion.indexOf("</strong>")).trim(); LOGGER.debug("last Version=" + lastVersion); } if (!lastVersion.equals(G15LastfmPlayer.getVersion())) LOGGER.debug("Not necessary to update"); else { LOGGER.debug("New update found!"); SwingUtilities.invokeLater(new Runnable() { @Override public void run() { if (JOptionPane.showConfirmDialog(null, "New version of G15Lastfm is available to download!", "New Update for G15Lastfm", JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) { LOGGER.debug("User choose to update, opening browser."); Desktop desktop = Desktop.getDesktop(); try { desktop.browse(new URI("http://code.google.com/p/g15lastfm/")); } catch (IOException e) { LOGGER.debug(e); } catch (URISyntaxException e) { LOGGER.debug(e); } } else { LOGGER.debug("User choose to not update."); } } }); } } catch (Exception e) { LOGGER.debug(e); } } }.start(); } | 885,722 |
0 | public void resumereceive(HttpServletRequest req, HttpServletResponse resp, SessionCommand command) { setHeader(resp); try { logger.debug("ResRec: Resume a 'receive' session with session id " + command.getSession() + " this client already received " + command.getLen() + " bytes"); File tempFile = new File(this.getSyncWorkDirectory(req), command.getSession() + ".smodif"); if (!tempFile.exists()) { logger.debug("ResRec: the file doesn't exist, so we created it by serializing the entities"); try { OutputStream fos = new FileOutputStream(tempFile); syncServer.getServerModifications(command.getSession(), fos); fos.close(); } catch (ImogSerializationException mse) { logger.error(mse.getMessage(), mse); } } InputStream fis = new FileInputStream(tempFile); fis.skip(command.getLen()); resp.setContentLength(fis.available()); while (fis.available() > 0) { resp.getOutputStream().write(fis.read()); } resp.getOutputStream().flush(); resp.flushBuffer(); fis.close(); } catch (IOException ioe) { logger.error(ioe.getMessage()); } } | public static void main(String[] args) { Stopwatch.start(""); HtmlParser parser = new HtmlParser(); try { Stopwatch.printTimeReset("", "> ParserDelegator"); ParserDelegator del = new ParserDelegator(); Stopwatch.printTimeReset("", "> url"); URL url = new URL(args[0]); Stopwatch.printTimeReset("", "> openStrem"); InputStream is = url.openStream(); Stopwatch.printTimeReset("", "< parse"); del.parse(new InputStreamReader(is), parser, true); Stopwatch.printTimeReset("", "< parse"); } catch (Throwable t) { t.printStackTrace(); } Stopwatch.printTimeReset("", "> traversal"); TreeTraversal.traverse(parser.startTag, "eachChild", new Function() { String lastPath = null; public void apply(Object obj) { if (obj instanceof String) { System.out.print(lastPath + ":"); System.out.println(obj); return; } Tag t = (Tag) obj; lastPath = Utils.tagPath(t); System.out.println(lastPath); } }); Stopwatch.printTimeReset("", "< traversal"); } | 885,723 |
1 | public void setTableBraille(String tableBraille, boolean sys) { fiConf.setProperty(OptNames.fi_braille_table, tableBraille); fiConf.setProperty(OptNames.fi_is_sys_braille_table, Boolean.toString(sys)); FileChannel in = null; FileChannel out = null; try { String fichTable; if (!(tableBraille.endsWith(".ent"))) { tableBraille = tableBraille + ".ent"; } if (sys) { fichTable = ConfigNat.getInstallFolder() + "xsl/tablesBraille/" + tableBraille; } else { fichTable = ConfigNat.getUserBrailleTableFolder() + tableBraille; } in = new FileInputStream(fichTable).getChannel(); out = new FileOutputStream(getUserBrailleTableFolder() + "Brltab.ent").getChannel(); in.transferTo(0, in.size(), out); in.close(); out.close(); } catch (IOException e) { e.printStackTrace(); } try { String fichTable; if (sys) { fichTable = ConfigNat.getInstallFolder() + "/xsl/tablesEmbosseuse/" + tableBraille; } else { fichTable = ConfigNat.getUserEmbossTableFolder() + "/" + tableBraille; } in = new FileInputStream(fichTable).getChannel(); out = new FileOutputStream(ConfigNat.getUserTempFolder() + "Table_pour_chaines.ent").getChannel(); in.transferTo(0, in.size(), out); in.close(); out.close(); } catch (IOException e) { e.printStackTrace(); } } | private String unJar(String jarPath, String jarEntry) { String path; if (jarPath.lastIndexOf("lib/") >= 0) path = jarPath.substring(0, jarPath.lastIndexOf("lib/")); else path = jarPath.substring(0, jarPath.lastIndexOf("/")); String relPath = jarEntry.substring(0, jarEntry.lastIndexOf("/")); try { new File(path + "/" + relPath).mkdirs(); JarFile jar = new JarFile(jarPath); ZipEntry ze = jar.getEntry(jarEntry); File bin = new File(path + "/" + jarEntry); IOUtils.copy(jar.getInputStream(ze), new FileOutputStream(bin)); } catch (Exception e) { e.printStackTrace(); } return path + "/" + jarEntry; } | 885,724 |
1 | private static void copy(String sourceName, String destName) throws IOException { File source = new File(sourceName); File dest = new File(destName); FileChannel in = null, out = null; try { in = new FileInputStream(source).getChannel(); out = new FileOutputStream(dest).getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); } finally { if (in != null) in.close(); if (out != null) out.close(); } } | public void encryptFile(String originalFile, String encryptedFile, String password) throws Exception { CipherOutputStream out; InputStream in; Cipher cipher; SecretKey key; byte[] byteBuffer; cipher = Cipher.getInstance("DES"); key = new SecretKeySpec(password.getBytes(), "DES"); cipher.init(Cipher.ENCRYPT_MODE, key); in = new FileInputStream(originalFile); out = new CipherOutputStream(new FileOutputStream(encryptedFile), cipher); byteBuffer = new byte[1024]; for (int n; (n = in.read(byteBuffer)) != -1; out.write(byteBuffer, 0, n)) ; in.close(); out.close(); } | 885,725 |
0 | public synchronized String encrypt(String plaintext) throws SystemUnavailableException { MessageDigest md = null; try { md = MessageDigest.getInstance("SHA"); } catch (NoSuchAlgorithmException e) { throw new SystemUnavailableException(e.getMessage()); } try { md.update(plaintext.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { throw new SystemUnavailableException(e.getMessage()); } byte raw[] = md.digest(); String hash = (new BASE64Encoder()).encode(raw); return hash; } | public static Collection<String> readXML(Bundle declaringBundle, URL url) throws XmlPullParserException { try { return readXML(declaringBundle, url.openStream()); } catch (IOException e) { throw new XmlPullParserException("Could not open \"" + url + "\" got exception:" + e.getLocalizedMessage()); } } | 885,726 |
1 | private static void processFile(StreamDriver driver, String sourceName) throws Exception { String destName = sourceName + ".xml"; File dest = new File(destName); if (dest.exists()) { throw new IllegalArgumentException("File '" + destName + "' already exists!"); } FileChannel sourceChannel = new FileInputStream(sourceName).getChannel(); try { MappedByteBuffer sourceByteBuffer = sourceChannel.map(FileChannel.MapMode.READ_ONLY, 0, sourceChannel.size()); CharsetDecoder decoder = Charset.forName("ISO-8859-15").newDecoder(); CharBuffer sourceBuffer = decoder.decode(sourceByteBuffer); driver.generateXmlDocument(sourceBuffer, new FileOutputStream(dest)); } finally { sourceChannel.close(); } } | public void merge(VMImage image, VMSnapShot another) throws VMException { if (path == null || another.getPath() == null) throw new VMException("EmuVMSnapShot is NULL!"); logging.debug(LOG_NAME, "merge images " + path + " and " + another.getPath()); File target = new File(path); File src = new File(another.getPath()); if (target.isDirectory() || src.isDirectory()) return; try { FileInputStream in = new FileInputStream(another.getPath()); FileChannel inChannel = in.getChannel(); FileOutputStream out = new FileOutputStream(path, true); FileChannel outChannel = out.getChannel(); outChannel.transferFrom(inChannel, 0, inChannel.size()); outChannel.close(); inChannel.close(); } catch (IOException e) { throw new VMException(e); } } | 885,727 |
1 | public static String generateHash(String message) throws NoSuchAlgorithmException, UnsupportedEncodingException, DigestException { MessageDigest digest; digest = MessageDigest.getInstance("SHA-1"); digest.reset(); digest.update(message.getBytes("iso-8859-1"), 0, message.length()); byte[] output = new byte[20]; digest.digest(output, 0, output.length); return convertToHex(output); } | private String hash(String text) throws NoSuchAlgorithmException { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(text.getBytes()); BigInteger hash = new BigInteger(1, md5.digest()); return hash.toString(16); } | 885,728 |
1 | public static void copyFile(File sourceFile, File targetFile) throws FileCopyingException { try { FileInputStream inputStream = new FileInputStream(sourceFile); FileOutputStream outputStream = new FileOutputStream(targetFile); FileChannel readableChannel = inputStream.getChannel(); FileChannel writableChannel = outputStream.getChannel(); writableChannel.truncate(0); writableChannel.transferFrom(readableChannel, 0, readableChannel.size()); inputStream.close(); outputStream.close(); } catch (IOException ioException) { String exceptionMessage = "An error occurred when copying from the file \"" + sourceFile.getAbsolutePath() + "\" to the file \"" + targetFile.getAbsolutePath() + "\"."; throw new FileCopyingException(exceptionMessage, ioException); } } | private void copyFile(File source, File target) throws IOException { FileChannel srcChannel = new FileInputStream(source).getChannel(); FileChannel dstChannel = new FileOutputStream(target).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } | 885,729 |
1 | @Override public JSONObject runCommand(JSONObject payload, HttpSession session) throws DefinedException { String sessionId = session.getId(); log.debug("Login -> runCommand SID: " + sessionId); JSONObject toReturn = new JSONObject(); boolean isOK = true; String username = null; try { username = payload.getString(ComConstants.LogIn.Request.USERNAME); } catch (JSONException e) { log.error("SessionId=" + sessionId + ", Missing username parameter", e); throw new DefinedException(StatusCodesV2.PARAMETER_ERROR); } String password = null; if (isOK) { try { password = payload.getString(ComConstants.LogIn.Request.PASSWORD); } catch (JSONException e) { log.error("SessionId=" + sessionId + ", Missing password parameter", e); throw new DefinedException(StatusCodesV2.PARAMETER_ERROR); } } if (isOK) { MessageDigest m = null; try { m = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { log.error("SessionId=" + sessionId + ", MD5 algorithm does not exist", e); e.printStackTrace(); throw new DefinedException(StatusCodesV2.INTERNAL_SYSTEM_FAILURE); } m.update(password.getBytes(), 0, password.length()); password = new BigInteger(1, m.digest()).toString(16); UserSession userSession = pli.login(username, password); try { if (userSession != null) { session.setAttribute("user", userSession); toReturn.put(ComConstants.Response.STATUS_CODE, StatusCodesV2.LOGIN_OK.getStatusCode()); toReturn.put(ComConstants.Response.STATUS_MESSAGE, StatusCodesV2.LOGIN_OK.getStatusMessage()); } else { log.error("SessionId=" + sessionId + ", Login failed: username=" + username + " not found"); toReturn.put(ComConstants.Response.STATUS_CODE, StatusCodesV2.LOGIN_USER_OR_PASSWORD_INCORRECT.getStatusCode()); toReturn.put(ComConstants.Response.STATUS_MESSAGE, StatusCodesV2.LOGIN_USER_OR_PASSWORD_INCORRECT.getStatusMessage()); } } catch (JSONException e) { log.error("SessionId=" + sessionId + ", JSON exception occured in response", e); e.printStackTrace(); throw new DefinedException(StatusCodesV2.INTERNAL_SYSTEM_FAILURE); } } log.debug("Login <- runCommand SID: " + sessionId); return toReturn; } | public static byte[] SHA1(String... strings) { try { MessageDigest digest = MessageDigest.getInstance("SHA1"); digest.reset(); for (String string : strings) { digest.update(string.getBytes("UTF-8")); } return digest.digest(); } catch (NoSuchAlgorithmException e) { throw new RuntimeException(e.toString(), e); } catch (UnsupportedEncodingException e) { throw new RuntimeException(e.toString(), e); } } | 885,730 |
0 | public static int gzipFile(File file_input, String file_output) { File gzip_output = new File(file_output); GZIPOutputStream gzip_out_stream; try { FileOutputStream out = new FileOutputStream(gzip_output); gzip_out_stream = new GZIPOutputStream(new BufferedOutputStream(out)); } catch (IOException e) { return STATUS_OUT_FAIL; } byte[] input_buffer = new byte[BUF_SIZE]; int len = 0; try { FileInputStream in = new FileInputStream(file_input); BufferedInputStream source = new BufferedInputStream(in, BUF_SIZE); while ((len = source.read(input_buffer, 0, BUF_SIZE)) != -1) gzip_out_stream.write(input_buffer, 0, len); in.close(); } catch (IOException e) { return STATUS_GZIP_FAIL; } try { gzip_out_stream.close(); } catch (IOException e) { } return STATUS_OK; } | public static void readTestData(String getDkpUrl) throws Exception { final URL url = new URL(getDkpUrl); final InputStream is = url.openStream(); try { final LineNumberReader rd = new LineNumberReader(new BufferedReader(new InputStreamReader(is))); String line = rd.readLine(); while (line != null) { System.out.println(line); line = rd.readLine(); } } finally { is.close(); } } | 885,731 |
1 | private void processHelpFile() { InputStream in = null; if (line.hasOption("helpfile")) { OutputStream out = null; try { String filename = line.getOptionValue("helpfile"); in = new FileInputStream(filename); filename = filename.replace('\\', '/'); filename = filename.substring(filename.lastIndexOf('/') + 1); File outFile = new File(outputDir, filename); if (LOG.isInfoEnabled()) { LOG.info("Processing generated file " + outFile.getAbsolutePath()); } out = new FileOutputStream(outFile); baseProperties.setProperty("helpfile", filename); IOUtils.copy(in, out); } catch (FileNotFoundException e) { LOG.error(e.getMessage(), e); } catch (IOException e) { LOG.error(e.getMessage(), e); } finally { if (in != null) { try { in.close(); } catch (IOException e) { LOG.error(e.getMessage(), e); } } if (out != null) { try { out.close(); } catch (IOException e) { LOG.error(e.getMessage(), e); } } } return; } Properties props = new Properties(baseProperties); ClassLoader cl = this.getClass().getClassLoader(); Document doc = null; try { in = cl.getResourceAsStream(RESOURCE_PKG + "/help-doc.xml"); doc = XmlUtils.parse(in); } catch (XmlException e) { LOG.error(e.getMessage(), e); } finally { if (in != null) { try { in.close(); } catch (IOException e) { LOG.error(e.getMessage(), e); } } } transformResource(doc, "help-doc.xsl", props, "help-doc.html"); baseProperties.setProperty("helpfile", "help-doc.html"); } | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | 885,732 |
0 | private Document post(String location, String content) throws ApplicationException { Document doc = null; try { URL url = new URL(location); HttpURLConnection uc = (HttpURLConnection) url.openConnection(); uc.setRequestMethod("POST"); uc.setRequestProperty("Content-Type", "application/xml"); uc.setRequestProperty("X-POST_DATA_FORMAT", "xml"); uc.setDoOutput(true); OutputStreamWriter out = new OutputStreamWriter(uc.getOutputStream()); out.write("<request>"); out.write("<token>" + configuration.getBackpackPassword() + "</token>"); if (content != null) { out.write("<item><content>" + content + "</content></item>"); } out.write("</request>"); out.close(); doc = XmlUtils.readDocumentFromInputStream(uc.getInputStream()); System.out.println(XmlUtils.toString(doc)); } catch (IOException e) { e.printStackTrace(); throw new ApplicationException(e); } return doc; } | @Test public void test_lookupType_FullSearch_TwoWords() throws Exception { URL url = new URL(baseUrl + "/lookupType/deep+core"); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("GET"); connection.setRequestProperty("Accept", "application/json"); assertThat(connection.getResponseCode(), equalTo(200)); assertThat(getResponse(connection), equalTo("[{\"itemTypeID\":11395,\"itemCategoryID\":16,\"name\":\"Deep Core Mining\",\"icon\":\"50_11\"},{\"itemTypeID\":12108,\"itemCategoryID\":7,\"name\":\"Deep Core Mining Laser I\",\"icon\":\"35_01\",\"metaLevel\":0},{\"itemTypeID\":12109,\"itemCategoryID\":9,\"name\":\"Deep Core Mining Laser I Blueprint\",\"icon\":\"12_08\"},{\"itemTypeID\":18068,\"itemCategoryID\":7,\"name\":\"Modulated Deep Core Miner II\",\"icon\":\"35_01\",\"metaLevel\":5},{\"itemTypeID\":18069,\"itemCategoryID\":9,\"name\":\"Modulated Deep Core Miner II Blueprint\",\"icon\":\"12_08\"},{\"itemTypeID\":24305,\"itemCategoryID\":7,\"name\":\"Modulated Deep Core Strip Miner II\",\"icon\":\"49_05\",\"metaLevel\":5},{\"itemTypeID\":24306,\"itemCategoryID\":9,\"name\":\"Modulated Deep Core Strip Miner II Blueprint\",\"icon\":\"12_08\"},{\"itemTypeID\":28748,\"itemCategoryID\":7,\"name\":\"ORE Deep Core Mining Laser\",\"icon\":\"35_01\",\"metaLevel\":6}]")); assertThat(connection.getHeaderField("Content-Type"), equalTo("application/json; charset=utf-8")); } | 885,733 |
0 | private static byte[] calcMd5(String pass) { try { MessageDigest digest = java.security.MessageDigest.getInstance("MD5"); digest.update(pass.getBytes(), 0, pass.length()); byte[] hash = digest.digest(); return hash; } catch (NoSuchAlgorithmException e) { System.err.println("No MD5 algorithm found"); System.exit(1); } return null; } | public static void copy(FileInputStream source, FileOutputStream dest) throws IOException { FileChannel in = null, out = null; try { in = source.getChannel(); out = dest.getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); } finally { if (in != null) in.close(); if (out != null) out.close(); } } | 885,734 |
1 | public static void copy(File srcFile, File destFile) throws IOException { FileInputStream in = null; FileOutputStream out = null; try { in = new FileInputStream(srcFile); out = new FileOutputStream(destFile); final byte[] buf = new byte[4096]; int read; while ((read = in.read(buf)) >= 0) { out.write(buf, 0, read); } } finally { try { if (in != null) in.close(); } catch (IOException ioe) { } try { if (out != null) out.close(); } catch (IOException ioe) { } } } | private void removeSessionId(InputStream inputStream, Output output) throws IOException { String jsessionid = RewriteUtils.getSessionId(target); boolean textContentType = ResourceUtils.isTextContentType(httpClientResponse.getHeader(HttpHeaders.CONTENT_TYPE), target.getDriver().getConfiguration().getParsableContentTypes()); if (jsessionid == null || !textContentType) { IOUtils.copy(inputStream, output.getOutputStream()); } else { String charset = httpClientResponse.getContentCharset(); if (charset == null) { charset = "ISO-8859-1"; } String content = IOUtils.toString(inputStream, charset); content = removeSessionId(jsessionid, content); if (output.getHeader(HttpHeaders.CONTENT_LENGTH) != null) { output.setHeader(HttpHeaders.CONTENT_LENGTH, Integer.toString(content.length())); } OutputStream outputStream = output.getOutputStream(); IOUtils.write(content, outputStream, charset); } inputStream.close(); } | 885,735 |
0 | public static String sendGetRequest(String endpoint, String requestParameters) { if (endpoint == null) return null; String result = null; if (endpoint.startsWith("http://")) { try { StringBuffer data = new StringBuffer(); String urlStr = endpoint; if (requestParameters != null && requestParameters.length() > 0) { urlStr += "?" + requestParameters; } URL url = new URL(urlStr); URLConnection conn = url.openConnection(); BufferedReader rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); StringBuffer sb = new StringBuffer(); String line; while ((line = rd.readLine()) != null) { sb.append(line); } rd.close(); result = sb.toString(); } catch (Exception e) { Logger.getLogger(HTTPClient.class.getClass().getName()).log(Level.FINE, "Could not connect to URL, is the service online?"); } } return result; } | private HttpURLConnection prepare(URL url, String method) { if (this.username != null && this.password != null) { this.headers.put("Authorization", "Basic " + Codec.encodeBASE64(this.username + ":" + this.password)); } try { HttpURLConnection connection = (HttpURLConnection) url.openConnection(); checkFileBody(connection); connection.setRequestMethod(method); for (String key : this.headers.keySet()) { connection.setRequestProperty(key, headers.get(key)); } return connection; } catch (Exception e) { throw new RuntimeException(e); } } | 885,736 |
1 | private static void copyObjects(File[] source, String target) { for (int i = 0; i < source.length; i++) { try { File inputFile = source[i]; File outputFile = new File(target + source[i].getName()); FileReader in = new FileReader(inputFile); FileWriter out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (Exception ex) { Logger.error(ex.getClass() + " " + ex.getMessage()); for (int j = 0; j < ex.getStackTrace().length; j++) Logger.error(" " + ex.getStackTrace()[j].toString()); ex.printStackTrace(); } } } | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | 885,737 |
1 | public void unzip(final File outDir) throws IOException { ZipInputStream input = new ZipInputStream(new ByteArrayInputStream(this.bytes)); ZipEntry entry = input.getNextEntry(); while (entry != null) { entry = input.getNextEntry(); if (entry != null) { File file = this.createFile(outDir, entry.getName()); if (!entry.isDirectory()) { FileOutputStream output = new FileOutputStream(file); IOUtils.copy(input, output); output.close(); } } } input.close(); } | protected void createFile(File sourceActionDirectory, File destinationActionDirectory, LinkedList<String> segments) throws DuplicateActionFileException { File currentSrcDir = sourceActionDirectory; File currentDestDir = destinationActionDirectory; String segment = ""; for (int i = 0; i < segments.size() - 1; i++) { segment = segments.get(i); currentSrcDir = new File(currentSrcDir, segment); currentDestDir = new File(currentDestDir, segment); } if (currentSrcDir != null && currentDestDir != null) { File srcFile = new File(currentSrcDir, segments.getLast()); if (srcFile.exists()) { File destFile = new File(currentDestDir, segments.getLast()); if (destFile.exists()) { throw new DuplicateActionFileException(srcFile.toURI().toASCIIString()); } try { FileChannel srcChannel = new FileInputStream(srcFile).getChannel(); FileChannel destChannel = new FileOutputStream(destFile).getChannel(); ByteBuffer buffer = ByteBuffer.allocate((int) srcChannel.size()); while (srcChannel.position() < srcChannel.size()) { srcChannel.read(buffer); } srcChannel.close(); buffer.rewind(); destChannel.write(buffer); destChannel.close(); } catch (Exception ex) { ex.printStackTrace(); } } } } | 885,738 |
0 | public static String getMdPsw(String passwd) throws Exception { MessageDigest md; md = MessageDigest.getInstance("MD5"); byte[] md5hash = new byte[32]; md.update(passwd.getBytes("iso-8859-1"), 0, passwd.length()); md5hash = md.digest(); return convertToHex(md5hash); } | private InputStream loadSource(String url) throws ClientProtocolException, IOException { HttpClient httpclient = new DefaultHttpClient(); httpclient.getParams().setParameter(HTTP.USER_AGENT, "Mozilla/4.0 (compatible; MSIE 7.0b; Windows NT 6.0)"); HttpGet httpget = new HttpGet(url); HttpResponse response = httpclient.execute(httpget); HttpEntity entity = response.getEntity(); return entity.getContent(); } | 885,739 |
0 | public static void upload(FTPDetails ftpDetails) { FTPClient ftp = new FTPClient(); try { String host = ftpDetails.getHost(); logger.info("Connecting to ftp host: " + host); ftp.connect(host); logger.info("Received reply from ftp :" + ftp.getReplyString()); ftp.login(ftpDetails.getUserName(), ftpDetails.getPassword()); ftp.setFileType(FTP.BINARY_FILE_TYPE); ftp.makeDirectory(ftpDetails.getRemoterDirectory()); logger.info("Created directory :" + ftpDetails.getRemoterDirectory()); ftp.changeWorkingDirectory(ftpDetails.getRemoterDirectory()); BufferedInputStream ftpInput = new BufferedInputStream(new FileInputStream(new File(ftpDetails.getLocalFilePath()))); OutputStream storeFileStream = ftp.storeFileStream(ftpDetails.getRemoteFileName()); IOUtils.copy(ftpInput, storeFileStream); logger.info("Copied file : " + ftpDetails.getLocalFilePath() + " >>> " + host + ":/" + ftpDetails.getRemoterDirectory() + "/" + ftpDetails.getRemoteFileName()); ftpInput.close(); storeFileStream.close(); ftp.logout(); ftp.disconnect(); logger.info("Logged out. "); } catch (Exception e) { throw new RuntimeException(e); } } | @Override public void incluir(Cliente cliente) throws Exception { Connection connection = criaConexao(false); String sql = "insert into cliente select nextval('sq_cliente') as cod_cliente, ? as nome, ? as sexo, ?"; PreparedStatement stmt = null; try { stmt = connection.prepareStatement(sql); stmt.setString(1, cliente.getNome()); stmt.setString(2, cliente.getSexo()); stmt.setInt(3, cliente.getCidade().getCodCidade()); int retorno = stmt.executeUpdate(); if (retorno == 0) { connection.rollback(); throw new SQLException("Ocorreu um erro inesperado no momento de inserir dados de cliente no banco!"); } connection.commit(); } catch (SQLException e) { connection.rollback(); throw e; } finally { try { stmt.close(); this.fechaConexao(); } catch (SQLException e) { throw e; } } } | 885,740 |
0 | public synchronized String encrypt(String plaintext) throws ServiceRuntimeException { MessageDigest md = null; try { md = MessageDigest.getInstance("SHA"); } catch (NoSuchAlgorithmException e) { throw new ServiceRuntimeException(e.getMessage()); } try { md.update(plaintext.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { throw new ServiceRuntimeException(e.getMessage()); } byte raw[] = md.digest(); String hash = (new BASE64Encoder()).encode(raw); return hash; } | public void processDeleteHolding(Holding holdingBean, AuthSession authSession) { if (authSession == null) { return; } DatabaseAdapter dbDyn = null; PreparedStatement ps = null; try { dbDyn = DatabaseAdapter.getInstance(); if (holdingBean.getId() == null) throw new IllegalArgumentException("holdingId is null"); processDeleteRelatedCompany(dbDyn, holdingBean, authSession); String sql = "delete from WM_LIST_HOLDING " + "where ID_HOLDING=? and ID_HOLDING in "; switch(dbDyn.getFamaly()) { case DatabaseManager.MYSQL_FAMALY: String idList = authSession.getGrantedHoldingId(); sql += " (" + idList + ") "; break; default: sql += "(select z1.ID_ROAD from v$_read_list_road z1 where z1.user_login = ?)"; break; } ps = dbDyn.prepareStatement(sql); RsetTools.setLong(ps, 1, holdingBean.getId()); switch(dbDyn.getFamaly()) { case DatabaseManager.MYSQL_FAMALY: break; default: ps.setString(2, authSession.getUserLogin()); break; } int i1 = ps.executeUpdate(); if (log.isDebugEnabled()) log.debug("Count of deleted records - " + i1); dbDyn.commit(); } catch (Exception e) { try { if (dbDyn != null) dbDyn.rollback(); } catch (Exception e001) { } String es = "Error delete holding"; log.error(es, e); throw new IllegalStateException(es, e); } finally { DatabaseManager.close(dbDyn, ps); dbDyn = null; ps = null; } } | 885,741 |
0 | List HttpGet(URL url) throws IOException { List responseList = new ArrayList(); logInfo("HTTP GET: " + url); URLConnection con = url.openConnection(); con.setAllowUserInteraction(false); BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream())); String inputLine; while ((inputLine = in.readLine()) != null) responseList.add(inputLine); in.close(); return responseList; } | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | 885,742 |
0 | public void actionPerformed(ActionEvent e) { Object src = e.getSource(); if (src == submitButton) { SubmissionProfile profile = (SubmissionProfile) destinationCombo.getSelectedItem(); String uri = profile.endpoint; String authPoint = profile.authenticationPoint; String user = userIDField.getText(); String passwd = new String(passwordField.getPassword()); try { URL url = new URL(authPoint + "?username=" + user + "&password=" + passwd); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String line = ""; String text = ""; while ((line = reader.readLine()) != null) { text = text + line; } reader.close(); submit(uri, user); JOptionPane.showMessageDialog(null, "Submission accepted", "Success", JOptionPane.INFORMATION_MESSAGE); this.setVisible(false); this.dispose(); } catch (Exception ex) { ex.printStackTrace(); if (ex instanceof java.io.IOException) { String msg = ex.getMessage(); if (msg.indexOf("HTTP response code: 401") != -1) JOptionPane.showMessageDialog(null, "Invalid Username/Password", "Invalid Username/Password", JOptionPane.ERROR_MESSAGE); else if (msg.indexOf("HTTP response code: 404") != -1) { try { submit(uri, user); JOptionPane.showMessageDialog(null, "Submission accepted", "Success", JOptionPane.INFORMATION_MESSAGE); } catch (Exception exc) { exc.printStackTrace(); } } } } } else if (src == cancelButton) { this.setVisible(false); this.dispose(); } } | private String md5(String txt) { try { MessageDigest m = MessageDigest.getInstance("MD5"); m.update(txt.getBytes(), 0, txt.length()); return new BigInteger(1, m.digest()).toString(16); } catch (Exception e) { return "BAD MD5"; } } | 885,743 |
0 | public void insertStringInFile(String file, String textToInsert, long fromByte, long toByte) throws Exception { String tmpFile = file + ".tmp"; BufferedInputStream in = null; BufferedOutputStream out = null; long byteCount = 0; try { in = new BufferedInputStream(new FileInputStream(new File(file))); out = new BufferedOutputStream(new FileOutputStream(tmpFile)); long size = fromByte; byte[] buf = null; if (size == 0) { } else { buf = new byte[(int) size]; int length = -1; if ((length = in.read(buf)) != -1) { out.write(buf, 0, length); byteCount = byteCount + length; } else { String msg = "Failed to read the first '" + size + "' bytes of file '" + file + "'. This might be a programming error."; this.logger.warning(msg); throw new Exception(msg); } } buf = textToInsert.getBytes(); int length = buf.length; out.write(buf, 0, length); byteCount = byteCount + length; long skipLength = toByte - fromByte; long skippedBytes = in.skip(skipLength); if (skippedBytes == -1) { } else { buf = new byte[4096]; length = -1; while ((length = in.read(buf)) != -1) { out.write(buf, 0, length); byteCount = byteCount + length; } } in.close(); in = null; out.close(); out = null; File fileToDelete = new File(file); boolean wasDeleted = fileToDelete.delete(); if (!wasDeleted) { String msg = "Failed to delete the original file '" + file + "' to replace it with the modified file after text insertion."; this.logger.warning(msg); throw new Exception(msg); } File fileToRename = new File(tmpFile); boolean wasRenamed = fileToRename.renameTo(fileToDelete); if (!wasRenamed) { String msg = "Failed to rename tmp file '" + tmpFile + "' to the name of the original file '" + file + "'"; this.logger.warning(msg); throw new Exception(msg); } } catch (Exception e) { this.logger.log(Level.WARNING, "Failed to read/write file '" + file + "'.", e); throw e; } finally { if (in != null) { try { in.close(); } catch (IOException e) { this.logger.log(Level.FINEST, "Ignoring error closing input file '" + file + "'.", e); } } if (out != null) { try { out.close(); } catch (IOException e) { this.logger.log(Level.FINEST, "Ignoring error closing output file '" + tmpFile + "'.", e); } } } } | public static String getMD5(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("MD5"); byte[] md5hash = new byte[32]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); md5hash = md.digest(); return convertToHex(md5hash); } | 885,744 |
1 | public void SetRoles(Connection conn, User user, String[] roles) throws NpsException { if (!IsSysAdmin() && !IsLocalAdmin()) throw new NpsException(ErrorHelper.ACCESS_NOPRIVILEGE); PreparedStatement pstmt = null; ResultSet rs = null; try { String sql = "delete from userrole where userid=?"; pstmt = conn.prepareStatement(sql); pstmt.setString(1, user.id); pstmt.executeUpdate(); if (roles != null && roles.length > 0) { try { pstmt.close(); } catch (Exception e1) { } sql = "insert into userrole(userid,roleid) values(?,?)"; pstmt = conn.prepareStatement(sql); for (int i = 0; i < roles.length; i++) { if (roles[i] != null && roles[i].length() > 0) { pstmt.setString(1, user.GetId()); pstmt.setString(2, roles[i]); pstmt.executeUpdate(); } } } try { pstmt.close(); } catch (Exception e1) { } if (user.roles_by_name != null) user.roles_by_name.clear(); if (user.roles_by_id != null) user.roles_by_id.clear(); if (roles != null && roles.length > 0) { sql = "select b.* from UserRole a,Role b where a.roleid = b.id and a.userid=?"; pstmt = conn.prepareStatement(sql); pstmt.setString(1, user.id); rs = pstmt.executeQuery(); while (rs.next()) { if (user.roles_by_name == null) user.roles_by_name = new Hashtable(); if (user.roles_by_id == null) user.roles_by_id = new Hashtable(); user.roles_by_name.put(rs.getString("name"), rs.getString("id")); user.roles_by_id.put(rs.getString("id"), rs.getString("name")); } } } catch (Exception e) { try { conn.rollback(); } catch (Exception e1) { } nps.util.DefaultLog.error(e); } finally { if (rs != null) try { rs.close(); } catch (Exception e) { } if (pstmt != null) try { pstmt.close(); } catch (Exception e1) { } } } | public void criarQuestaoDiscursiva(QuestaoDiscursiva q) throws SQLException { PreparedStatement stmt = null; String sql = "INSERT INTO discursiva (id_questao,gabarito) VALUES (?,?)"; try { stmt = conexao.prepareStatement(sql); stmt.setInt(1, q.getIdQuestao()); stmt.setString(2, q.getGabarito()); stmt.executeUpdate(); conexao.commit(); } catch (SQLException e) { conexao.rollback(); throw e; } } | 885,745 |
0 | @Test public void testWriteAndReadBiggerUnbuffered() throws Exception { JCFSFileServer server = new JCFSFileServer(defaultTcpPort, defaultTcpAddress, defaultUdpPort, defaultUdpAddress, dir, 0, 0); JCFS.configureDiscovery(defaultUdpAddress, defaultUdpPort); try { server.start(); RFile file = new RFile("testreadwriteb.txt"); RFileOutputStream out = new RFileOutputStream(file); String body = ""; int size = 50 * 1024; for (int i = 0; i < size; i++) { body = body + "a"; } out.write(body.getBytes("utf-8")); out.close(); File expected = new File(dir, "testreadwriteb.txt"); assertTrue(expected.isFile()); assertEquals(body.length(), expected.length()); RFileInputStream in = new RFileInputStream(file); ByteArrayOutputStream tmp = new ByteArrayOutputStream(); int b = in.read(); while (b != -1) { tmp.write(b); b = in.read(); } byte[] buffer = tmp.toByteArray(); in.close(); assertEquals(body.length(), buffer.length); String resultRead = new String(buffer, "utf-8"); assertEquals(body, resultRead); } finally { server.stop(); } } | public void addPropertyColumns(WCAChannel destination, Set<Property> properties) throws SQLException { Session session = HibernateUtil.getSessionFactory().openSession(); Connection con = session.connection(); try { createPropertyTable(destination); extendPropertyList(destination, properties); Statement statement = con.createStatement(); for (Property property : properties) { String propertyName = removeBadChars(property.getName()); statement.executeUpdate(alterTable.format(new Object[] { getTableName(destination), propertyName, property.getDBColumnType() })); } con.commit(); con.close(); session.close(); } catch (SQLException e) { con.rollback(); session.close(); throw e; } } | 885,746 |
0 | public static String getMD5(final String data) { try { MessageDigest m = MessageDigest.getInstance("MD5"); m.reset(); m.update(data.getBytes()); BigInteger bigInt = new BigInteger(1, m.digest()); String hashtext = bigInt.toString(16); while (hashtext.length() < 32) { hashtext = "0" + hashtext; } return hashtext; } catch (NoSuchAlgorithmException e) { e.printStackTrace(); return e.getMessage(); } } | public void writeOutput(String directory) throws IOException { File f = new File(directory); int i = 0; if (f.isDirectory()) { for (AppInventorScreen screen : screens.values()) { File screenFile = new File(getScreenFilePath(f.getAbsolutePath(), screen)); screenFile.getParentFile().mkdirs(); screenFile.createNewFile(); FileWriter out = new FileWriter(screenFile); String initial = files.get(i).toString(); Map<String, String> types = screen.getTypes(); String[] lines = initial.split("\n"); for (String key : types.keySet()) { if (!key.trim().equals(screen.getName().trim())) { String value = types.get(key); boolean varFound = false; boolean importFound = false; for (String line : lines) { if (line.matches("^\\s*(public|private)\\s+" + value + "\\s+" + key + "\\s*=.*;$")) varFound = true; if (line.matches("^\\s*(public|private)\\s+" + value + "\\s+" + key + "\\s*;$")) varFound = true; if (line.matches("^\\s*import\\s+.*" + value + "\\s*;$")) importFound = true; } if (!varFound) initial = initial.replaceFirst("(?s)(?<=\\{\n)", "\tprivate " + value + " " + key + ";\n"); if (!importFound) initial = initial.replaceFirst("(?=import)", "import com.google.devtools.simple.runtime.components.android." + value + ";\n"); } } out.write(initial); out.close(); i++; } File manifestFile = new File(getManifestFilePath(f.getAbsolutePath(), manifest)); manifestFile.getParentFile().mkdirs(); manifestFile.createNewFile(); FileWriter out = new FileWriter(manifestFile); out.write(manifest.toString()); out.close(); File projectFile = new File(getProjectFilePath(f.getAbsolutePath(), project)); projectFile.getParentFile().mkdirs(); projectFile.createNewFile(); out = new FileWriter(projectFile); out.write(project.toString()); out.close(); String[] copyResourceFilenames = { "proguard.cfg", "project.properties", "libSimpleAndroidRuntime.jar", "\\.classpath", "res/drawable/icon.png", "\\.settings/org.eclipse.jdt.core.prefs" }; for (String copyResourceFilename : copyResourceFilenames) { InputStream is = getClass().getResourceAsStream("/resources/" + copyResourceFilename.replace("\\.", "")); File outputFile = new File(f.getAbsoluteFile() + File.separator + copyResourceFilename.replace("\\.", ".")); outputFile.getParentFile().mkdirs(); OutputStream os = new FileOutputStream(outputFile); byte[] buf = new byte[1024]; int readBytes; if (is == null) System.out.println("/resources/" + copyResourceFilename.replace("\\.", "")); if (os == null) System.out.println(f.getAbsolutePath() + File.separator + copyResourceFilename.replace("\\.", ".")); while ((readBytes = is.read(buf)) > 0) { os.write(buf, 0, readBytes); } } for (String assetName : assets) { InputStream is = new FileInputStream(new File(assetsDir.getAbsolutePath() + File.separator + assetName)); File outputFile = new File(f.getAbsoluteFile() + File.separator + assetName); outputFile.getParentFile().mkdirs(); OutputStream os = new FileOutputStream(outputFile); byte[] buf = new byte[1024]; int readBytes; while ((readBytes = is.read(buf)) > 0) { os.write(buf, 0, readBytes); } } File assetsOutput = new File(getAssetsFilePath(f.getAbsolutePath())); new File(assetsDir.getAbsoluteFile() + File.separator + "assets").renameTo(assetsOutput); } } | 885,747 |
0 | private void album(String albumTitle, String albumNbSong, URL url) { try { if (color == SWT.COLOR_WHITE) { color = SWT.COLOR_GRAY; } else { color = SWT.COLOR_WHITE; } url.openConnection(); InputStream is = url.openStream(); Image coverPicture = new Image(this.getDisplay(), is); Composite albumComposite = new Composite(main, SWT.NONE); albumComposite.setLayout(new FormLayout()); FormData data = new FormData(); data.left = new FormAttachment(0, 5); data.right = new FormAttachment(100, -5); if (prevCompo == null) { data.top = new FormAttachment(0, 0); } else { data.top = new FormAttachment(prevCompo, 0, SWT.BOTTOM); } albumComposite.setLayoutData(data); albumComposite.setBackground(Display.getDefault().getSystemColor(color)); Label cover = new Label(albumComposite, SWT.LEFT); cover.setText("cover"); cover.setImage(coverPicture); data = new FormData(75, 75); cover.setLayoutData(data); Label title = new Label(albumComposite, SWT.CENTER); title.setFont(new Font(this.getDisplay(), "Arial", 10, SWT.BOLD)); title.setText(albumTitle); data = new FormData(); data.bottom = new FormAttachment(50, -5); data.left = new FormAttachment(cover, 5); title.setBackground(Display.getDefault().getSystemColor(color)); title.setLayoutData(data); Label nbSong = new Label(albumComposite, SWT.LEFT | SWT.BOLD); nbSong.setFont(new Font(this.getDisplay(), "Arial", 8, SWT.ITALIC)); nbSong.setText("Release date : " + albumNbSong); data = new FormData(); data.top = new FormAttachment(50, 5); data.left = new FormAttachment(cover, 5); nbSong.setBackground(Display.getDefault().getSystemColor(color)); nbSong.setLayoutData(data); prevCompo = albumComposite; } catch (Exception e) { e.printStackTrace(); } } | public static boolean update(Cargo cargo) { int result = 0; Connection c = DBConnection.getConnection(); PreparedStatement pst = null; if (c == null) { return false; } try { c.setAutoCommit(false); String sql = "update cargo set nome = (?) where id_cargo= ?"; pst = c.prepareStatement(sql); pst.setString(1, cargo.getNome()); pst.setInt(2, cargo.getCodigo()); result = pst.executeUpdate(); c.commit(); } catch (SQLException e) { try { c.rollback(); } catch (SQLException e1) { e1.printStackTrace(); } System.out.println("[CargoDAO.update] Erro ao atualizar -> " + e.getMessage()); } finally { DBConnection.closePreparedStatement(pst); DBConnection.closeConnection(c); } if (result > 0) { return true; } else { return false; } } | 885,748 |
0 | public static boolean installMetricsCfg(Db db, String xmlFileName) throws Exception { String xmlText = FileHelper.asString(xmlFileName); Bundle bundle = new Bundle(); loadMetricsCfg(bundle, xmlFileName, xmlText); try { db.begin(); PreparedStatement psExists = db.prepareStatement("SELECT e_bundle_id, xml_decl_path, xml_text FROM sdw.e_bundle WHERE xml_decl_path = ?;"); psExists.setString(1, xmlFileName); ResultSet rsExists = db.executeQuery(psExists); if (rsExists.next()) { db.rollback(); return false; } PreparedStatement psId = db.prepareStatement("SELECT currval('sdw.e_bundle_serial');"); PreparedStatement psAdd = db.prepareStatement("INSERT INTO sdw.e_bundle (xml_decl_path, xml_text, sdw_major_version, sdw_minor_version, file_major_version, file_minor_version) VALUES (?, ?, ?, ?, ?, ?);"); psAdd.setString(1, xmlFileName); psAdd.setString(2, xmlText); FileInformation fi = bundle.getSingleFileInformation(); if (!xmlFileName.equals(fi.filename)) throw new IllegalStateException("FileInformation bad for " + xmlFileName); psAdd.setInt(3, Globals.SDW_MAJOR_VER); psAdd.setInt(4, Globals.SDW_MINOR_VER); psAdd.setInt(5, fi.majorVer); psAdd.setInt(6, fi.minorVer); if (1 != db.executeUpdate(psAdd)) { throw new IllegalStateException("Could not add " + xmlFileName); } int bundleId = DbHelper.getIntKey(psId); PreparedStatement psGroupId = db.prepareStatement("SELECT currval('sdw.e_metric_group_serial');"); PreparedStatement psAddGroup = db.prepareStatement("INSERT INTO sdw.e_metric_group (bundle_id, metric_group_name) VALUES (?, ?);"); psAddGroup.setInt(1, bundleId); PreparedStatement psMetricId = db.prepareStatement("SELECT currval('sdw.e_metric_name_serial');"); PreparedStatement psAddMetric = db.prepareStatement("INSERT INTO sdw.e_metric_name (bundle_id, metric_name) VALUES (?, ?);"); psAddMetric.setInt(1, bundleId); PreparedStatement psAddGroup2Metric = db.prepareStatement("INSERT INTO sdw.e_metric_groups (metric_name_id, metric_group_id) VALUES (?, ?);"); Iterator<MetricGroup> i = bundle.getAllMetricGroups(); while (i.hasNext()) { MetricGroup grp = i.next(); psAddGroup.setString(2, grp.groupName); if (1 != db.executeUpdate(psAddGroup)) throw new IllegalStateException("Could not add group " + grp.groupName + " from " + xmlFileName); int groupId = DbHelper.getIntKey(psGroupId); psAddGroup2Metric.setInt(2, groupId); Iterator<String> j = grp.getAllMetricNames(); while (j.hasNext()) { String metricName = j.next(); psAddMetric.setString(2, metricName); if (1 != db.executeUpdate(psAddMetric)) throw new IllegalStateException("Could not add " + metricName + " from " + xmlFileName); int metricId = DbHelper.getIntKey(psMetricId); psAddGroup2Metric.setInt(1, metricId); if (1 != db.executeUpdate(psAddGroup2Metric)) throw new IllegalStateException("Could not add group " + grp.groupName + " -> " + metricName + " from " + xmlFileName); } } return true; } catch (Exception e) { db.rollback(); throw e; } finally { db.commitUnless(); } } | private LinkedList<Datum> processDatum(Datum dataset) { ArrayList<Object[]> markerTestResults = new ArrayList<Object[]>(); ArrayList<Object[]> alleleEstimateResults = new ArrayList<Object[]>(); boolean hasAlleleNames = false; String blank = new String(""); MarkerPhenotypeAdapter theAdapter; if (dataset.getDataType().equals(MarkerPhenotype.class)) { theAdapter = new MarkerPhenotypeAdapter((MarkerPhenotype) dataset.getData()); } else theAdapter = new MarkerPhenotypeAdapter((Phenotype) dataset.getData()); int numberOfMarkers = theAdapter.getNumberOfMarkers(); if (numberOfMarkers == 0) { return calculateBLUEsFromPhenotypes(theAdapter, dataset.getName()); } int numberOfCovariates = theAdapter.getNumberOfCovariates(); int numberOfFactors = theAdapter.getNumberOfFactors(); int numberOfPhenotypes = theAdapter.getNumberOfPhenotypes(); int expectedIterations = numberOfPhenotypes * numberOfMarkers; int iterationsSofar = 0; int percentFinished = 0; File tempFile = null; File ftestFile = null; File blueFile = null; BufferedWriter ftestWriter = null; BufferedWriter BLUEWriter = null; String ftestHeader = "Trait\tMarker\tLocus\tLocus_pos\tChr\tChr_pos\tmarker_F\tmarker_p\tperm_p\tmarkerR2\tmarkerDF\tmarkerMS\terrorDF\terrorMS\tmodelDF\tmodelMS"; String BLUEHeader = "Trait\tMarker\tObs\tLocus\tLocus_pos\tChr\tChr_pos\tAllele\tEstimate"; if (writeOutputToFile) { String outputbase = outputName; if (outputbase.endsWith(".txt")) { int index = outputbase.lastIndexOf("."); outputbase = outputbase.substring(0, index); } String datasetNameNoSpace = dataset.getName().trim().replaceAll("\\ ", "_"); ftestFile = new File(outputbase + "_" + datasetNameNoSpace + "_ftest.txt"); int count = 0; while (ftestFile.exists()) { count++; ftestFile = new File(outputbase + "_" + datasetNameNoSpace + "_ftest" + count + ".txt"); } blueFile = new File(outputbase + "_" + datasetNameNoSpace + "_BLUEs.txt"); count = 0; while (blueFile.exists()) { count++; blueFile = new File(outputbase + "_" + datasetNameNoSpace + "_BLUEs" + count + ".txt"); } tempFile = new File(outputbase + "_" + datasetNameNoSpace + "_ftest.tmp"); try { if (permute) { ftestWriter = new BufferedWriter(new FileWriter(tempFile)); ftestWriter.write(ftestHeader); ftestWriter.newLine(); } else { ftestWriter = new BufferedWriter(new FileWriter(ftestFile)); ftestWriter.write(ftestHeader); ftestWriter.newLine(); } if (reportBLUEs) { BLUEWriter = new BufferedWriter(new FileWriter(blueFile)); BLUEWriter.write(BLUEHeader); BLUEWriter.newLine(); } } catch (IOException e) { myLogger.error("Failed to open file for output"); myLogger.error(e); return null; } } if (permute) { minP = new double[numberOfPhenotypes][numberOfPermutations]; for (int i = 0; i < numberOfPermutations; i++) { for (int j = 0; j < numberOfPhenotypes; j++) { minP[j][i] = 1; } } } for (int ph = 0; ph < numberOfPhenotypes; ph++) { double[] phenotypeData = theAdapter.getPhenotypeValues(ph); boolean[] missing = theAdapter.getMissingPhenotypes(ph); ArrayList<String[]> factorList = MarkerPhenotypeAdapterUtils.getFactorList(theAdapter, ph, missing); ArrayList<double[]> covariateList = MarkerPhenotypeAdapterUtils.getCovariateList(theAdapter, ph, missing); double[][] permutedData = null; if (permute) { permutedData = permuteData(phenotypeData, missing, factorList, covariateList, theAdapter); } for (int m = 0; m < numberOfMarkers; m++) { Object[] markerData = theAdapter.getMarkerValue(ph, m); boolean[] finalMissing = new boolean[missing.length]; System.arraycopy(missing, 0, finalMissing, 0, missing.length); MarkerPhenotypeAdapterUtils.updateMissing(finalMissing, theAdapter.getMissingMarkers(ph, m)); int[] nonmissingRows = MarkerPhenotypeAdapterUtils.getNonMissingIndex(finalMissing); int numberOfObs = nonmissingRows.length; double[] y = new double[numberOfObs]; for (int i = 0; i < numberOfObs; i++) y[i] = phenotypeData[nonmissingRows[i]]; int firstMarkerAlleleEstimate = 1; ArrayList<ModelEffect> modelEffects = new ArrayList<ModelEffect>(); FactorModelEffect meanEffect = new FactorModelEffect(new int[numberOfObs], false); meanEffect.setID("mean"); modelEffects.add(meanEffect); if (numberOfFactors > 0) { for (int f = 0; f < numberOfFactors; f++) { String[] afactor = factorList.get(f); String[] factorLabels = new String[numberOfObs]; for (int i = 0; i < numberOfObs; i++) factorLabels[i] = afactor[nonmissingRows[i]]; FactorModelEffect fme = new FactorModelEffect(ModelEffectUtils.getIntegerLevels(factorLabels), true, theAdapter.getFactorName(f)); modelEffects.add(fme); firstMarkerAlleleEstimate += fme.getNumberOfLevels() - 1; } } if (numberOfCovariates > 0) { for (int c = 0; c < numberOfCovariates; c++) { double[] covar = new double[numberOfObs]; double[] covariateData = covariateList.get(c); for (int i = 0; i < numberOfObs; i++) covar[i] = covariateData[nonmissingRows[i]]; modelEffects.add(new CovariateModelEffect(covar, theAdapter.getCovariateName(c))); firstMarkerAlleleEstimate++; } } ModelEffect markerEffect; boolean markerIsDiscrete = theAdapter.isMarkerDiscrete(m); ArrayList<Object> alleleNames = new ArrayList<Object>(); if (markerIsDiscrete) { Object[] markers = new Object[numberOfObs]; for (int i = 0; i < numberOfObs; i++) markers[i] = markerData[nonmissingRows[i]]; int[] markerLevels = ModelEffectUtils.getIntegerLevels(markers, alleleNames); markerEffect = new FactorModelEffect(markerLevels, true, theAdapter.getMarkerName(m)); hasAlleleNames = true; } else { double[] markerdbl = new double[numberOfObs]; for (int i = 0; i < numberOfObs; i++) markerdbl[i] = ((Double) markerData[nonmissingRows[i]]).doubleValue(); markerEffect = new CovariateModelEffect(markerdbl, theAdapter.getMarkerName(m)); } int[] alleleCounts = markerEffect.getLevelCounts(); modelEffects.add(markerEffect); int markerEffectNumber = modelEffects.size() - 1; Identifier[] taxaSublist = new Identifier[numberOfObs]; Identifier[] taxa = theAdapter.getTaxa(ph); for (int i = 0; i < numberOfObs; i++) taxaSublist[i] = taxa[nonmissingRows[i]]; boolean areTaxaReplicated = containsDuplicates(taxaSublist); double[] markerSSdf = null, errorSSdf = null, modelSSdf = null; double F, p; double[] beta = null; if (areTaxaReplicated && markerIsDiscrete) { ModelEffect taxaEffect = new FactorModelEffect(ModelEffectUtils.getIntegerLevels(taxaSublist), true); modelEffects.add(taxaEffect); SweepFastNestedModel sfnm = new SweepFastNestedModel(modelEffects, y); double[] taxaSSdf = sfnm.getTaxaInMarkerSSdf(); double[] residualSSdf = sfnm.getErrorSSdf(); markerSSdf = sfnm.getMarkerSSdf(); errorSSdf = sfnm.getErrorSSdf(); modelSSdf = sfnm.getModelcfmSSdf(); F = markerSSdf[0] / markerSSdf[1] / taxaSSdf[0] * taxaSSdf[1]; try { p = LinearModelUtils.Ftest(F, markerSSdf[1], taxaSSdf[1]); } catch (Exception e) { p = Double.NaN; } beta = sfnm.getBeta(); int markerdf = (int) markerSSdf[1]; if (permute && markerdf > 0) { updatePermutationPValues(ph, permutedData, nonMissingIndex(missing, finalMissing), getXfromModelEffects(modelEffects), sfnm.getInverseOfXtX(), markerdf); } } else { SweepFastLinearModel sflm = new SweepFastLinearModel(modelEffects, y); modelSSdf = sflm.getModelcfmSSdf(); markerSSdf = sflm.getMarginalSSdf(markerEffectNumber); errorSSdf = sflm.getResidualSSdf(); F = markerSSdf[0] / markerSSdf[1] / errorSSdf[0] * errorSSdf[1]; try { p = LinearModelUtils.Ftest(F, markerSSdf[1], errorSSdf[1]); } catch (Exception e) { p = Double.NaN; } beta = sflm.getBeta(); int markerdf = (int) markerSSdf[1]; if (permute && markerdf > 0) { updatePermutationPValues(ph, permutedData, nonMissingIndex(missing, finalMissing), getXfromModelEffects(modelEffects), sflm.getInverseOfXtX(), markerdf); } } if (!filterOutput || p < maxp) { String traitname = theAdapter.getPhenotypeName(ph); if (traitname == null) traitname = blank; String marker = theAdapter.getMarkerName(m); if (marker == null) marker = blank; String locus = theAdapter.getLocusName(m); Integer site = new Integer(theAdapter.getLocusPosition(m)); String chrname = ""; Double chrpos = Double.NaN; if (hasMap) { int ndx = -1; ndx = myMap.getMarkerIndex(marker); if (ndx > -1) { chrname = myMap.getChromosome(ndx); chrpos = myMap.getGeneticPosition(ndx); } } Object[] result = new Object[16]; int col = 0; result[col++] = traitname; result[col++] = marker; result[col++] = locus; result[col++] = site; result[col++] = chrname; result[col++] = chrpos; result[col++] = new Double(F); result[col++] = new Double(p); result[col++] = Double.NaN; result[col++] = new Double(markerSSdf[0] / (modelSSdf[0] + errorSSdf[0])); result[col++] = new Double(markerSSdf[1]); result[col++] = new Double(markerSSdf[0] / markerSSdf[1]); result[col++] = new Double(errorSSdf[1]); result[col++] = new Double(errorSSdf[0] / errorSSdf[1]); result[col++] = new Double(modelSSdf[1]); result[col++] = new Double(modelSSdf[0] / modelSSdf[1]); if (writeOutputToFile) { StringBuilder sb = new StringBuilder(); sb.append(result[0]); for (int i = 1; i < 16; i++) sb.append("\t").append(result[i]); try { ftestWriter.write(sb.toString()); ftestWriter.newLine(); } catch (IOException e) { myLogger.error("Failed to write output to ftest file. Ending prematurely"); try { ftestWriter.flush(); BLUEWriter.flush(); } catch (Exception e1) { } myLogger.error(e); return null; } } else { markerTestResults.add(result); } int numberOfMarkerAlleles = alleleNames.size(); if (numberOfMarkerAlleles == 0) numberOfMarkerAlleles++; for (int i = 0; i < numberOfMarkerAlleles; i++) { result = new Object[9]; result[0] = traitname; result[1] = marker; result[2] = new Integer(alleleCounts[i]); result[3] = locus; result[4] = site; result[5] = chrname; result[6] = chrpos; if (numberOfMarkerAlleles == 1) result[7] = ""; else result[7] = alleleNames.get(i); if (i == numberOfMarkerAlleles - 1) result[8] = 0.0; else result[8] = beta[firstMarkerAlleleEstimate + i]; if (writeOutputToFile) { StringBuilder sb = new StringBuilder(); sb.append(result[0]); for (int j = 1; j < 9; j++) sb.append("\t").append(result[j]); try { BLUEWriter.write(sb.toString()); BLUEWriter.newLine(); } catch (IOException e) { myLogger.error("Failed to write output to ftest file. Ending prematurely"); try { ftestWriter.flush(); BLUEWriter.flush(); } catch (Exception e1) { } myLogger.error(e); return null; } } else { alleleEstimateResults.add(result); } } } int tmpPercent = ++iterationsSofar * 100 / expectedIterations; if (tmpPercent > percentFinished) { percentFinished = tmpPercent; fireProgress(percentFinished); } } } fireProgress(0); if (writeOutputToFile) { try { ftestWriter.close(); BLUEWriter.close(); } catch (IOException e) { e.printStackTrace(); } } HashMap<String, Integer> traitnameMap = new HashMap<String, Integer>(); if (permute) { for (int ph = 0; ph < numberOfPhenotypes; ph++) { Arrays.sort(minP[ph]); traitnameMap.put(theAdapter.getPhenotypeName(ph), ph); } if (writeOutputToFile) { try { BufferedReader tempReader = new BufferedReader(new FileReader(tempFile)); ftestWriter = new BufferedWriter(new FileWriter(ftestFile)); ftestWriter.write(tempReader.readLine()); ftestWriter.newLine(); String input; String[] data; Pattern tab = Pattern.compile("\t"); while ((input = tempReader.readLine()) != null) { data = tab.split(input); String trait = data[0]; double pval = Double.parseDouble(data[7]); int ph = traitnameMap.get(trait); int ndx = Arrays.binarySearch(minP[ph], pval); if (ndx < 0) ndx = -ndx - 1; if (ndx == 0) ndx = 1; data[8] = Double.toString((double) ndx / (double) numberOfPermutations); ftestWriter.write(data[0]); for (int i = 1; i < data.length; i++) { ftestWriter.write("\t"); ftestWriter.write(data[i]); } ftestWriter.newLine(); } tempReader.close(); ftestWriter.close(); tempFile.delete(); } catch (IOException e) { myLogger.error(e); } } else { for (Object[] result : markerTestResults) { String trait = result[0].toString(); double pval = (Double) result[7]; int ph = traitnameMap.get(trait); int ndx = Arrays.binarySearch(minP[ph], pval); if (ndx < 0) ndx = -ndx - 1; if (ndx == 0) ndx = 1; result[8] = new Double((double) ndx / (double) numberOfPermutations); } } } String[] columnLabels = new String[] { "Trait", "Marker", "Locus", "Locus_pos", "Chr", "Chr_pos", "marker_F", "marker_p", "perm_p", "markerR2", "markerDF", "markerMS", "errorDF", "errorMS", "modelDF", "modelMS" }; boolean hasMarkerNames = theAdapter.hasMarkerNames(); LinkedList<Integer> outputList = new LinkedList<Integer>(); outputList.add(0); if (hasMarkerNames) outputList.add(1); outputList.add(2); outputList.add(3); if (hasMap) { outputList.add(4); outputList.add(5); } outputList.add(6); outputList.add(7); if (permute) outputList.add(8); for (int i = 9; i < 16; i++) outputList.add(i); LinkedList<Datum> resultset = new LinkedList<Datum>(); int nrows = markerTestResults.size(); Object[][] table = new Object[nrows][]; int numberOfColumns = outputList.size(); String[] colnames = new String[numberOfColumns]; int count = 0; for (Integer ndx : outputList) colnames[count++] = columnLabels[ndx]; for (int i = 0; i < nrows; i++) { table[i] = new Object[numberOfColumns]; Object[] result = markerTestResults.get(i); count = 0; for (Integer ndx : outputList) table[i][count++] = result[ndx]; } StringBuilder tableName = new StringBuilder("GLM_marker_test_"); tableName.append(dataset.getName()); StringBuilder comments = new StringBuilder("Tests of Marker-Phenotype Association"); comments.append("GLM: fixed effect linear model\n"); comments.append("Data set: ").append(dataset.getName()); comments.append("\nmodel: trait = mean"); for (int i = 0; i < theAdapter.getNumberOfFactors(); i++) { comments.append(" + "); comments.append(theAdapter.getFactorName(i)); } for (int i = 0; i < theAdapter.getNumberOfCovariates(); i++) { comments.append(" + "); comments.append(theAdapter.getCovariateName(i)); } comments.append(" + marker"); if (writeOutputToFile) { comments.append("\nOutput written to " + ftestFile.getPath()); } TableReport markerTestReport = new SimpleTableReport("Marker Test", colnames, table); resultset.add(new Datum(tableName.toString(), markerTestReport, comments.toString())); int[] outputIndex; columnLabels = new String[] { "Trait", "Marker", "Obs", "Locus", "Locus_pos", "Chr", "Chr_pos", "Allele", "Estimate" }; if (hasAlleleNames) { if (hasMarkerNames && hasMap) { outputIndex = new int[] { 0, 1, 2, 3, 4, 5, 6, 7, 8 }; } else if (hasMarkerNames) { outputIndex = new int[] { 0, 1, 2, 3, 4, 7, 8 }; } else if (hasMap) { outputIndex = new int[] { 0, 2, 3, 4, 5, 6, 7, 8 }; } else { outputIndex = new int[] { 0, 2, 3, 4, 7, 8 }; } } else { if (hasMarkerNames && hasMap) { outputIndex = new int[] { 0, 1, 2, 3, 4, 5, 6, 8 }; } else if (hasMarkerNames) { outputIndex = new int[] { 0, 1, 2, 3, 4, 8 }; } else if (hasMap) { outputIndex = new int[] { 0, 2, 3, 4, 5, 6, 8 }; } else { outputIndex = new int[] { 0, 2, 3, 4, 8 }; } } nrows = alleleEstimateResults.size(); table = new Object[nrows][]; numberOfColumns = outputIndex.length; colnames = new String[numberOfColumns]; for (int j = 0; j < numberOfColumns; j++) { colnames[j] = columnLabels[outputIndex[j]]; } for (int i = 0; i < nrows; i++) { table[i] = new Object[numberOfColumns]; Object[] result = alleleEstimateResults.get(i); for (int j = 0; j < numberOfColumns; j++) { table[i][j] = result[outputIndex[j]]; } } tableName = new StringBuilder("GLM allele estimates for "); tableName.append(dataset.getName()); comments = new StringBuilder("Marker allele effect estimates\n"); comments.append("GLM: fixed effect linear model\n"); comments.append("Data set: ").append(dataset.getName()); comments.append("\nmodel: trait = mean"); for (int i = 0; i < theAdapter.getNumberOfFactors(); i++) { comments.append(" + "); comments.append(theAdapter.getFactorName(i)); } for (int i = 0; i < theAdapter.getNumberOfCovariates(); i++) { comments.append(" + "); comments.append(theAdapter.getCovariateName(i)); } comments.append(" + marker"); if (writeOutputToFile) { comments.append("\nOutput written to " + blueFile.getPath()); } TableReport alleleEstimateReport = new SimpleTableReport("Allele Estimates", colnames, table); resultset.add(new Datum(tableName.toString(), alleleEstimateReport, comments.toString())); fireProgress(0); return resultset; } | 885,749 |
0 | public static final String enctrypt(String password) { MessageDigest md = null; byte[] byteHash = null; StringBuffer resultString = new StringBuffer(); try { md = MessageDigest.getInstance("SHA1"); } catch (NoSuchAlgorithmException e) { System.out.println("NoSuchAlgorithmException caught!"); throw new RuntimeException("NoSuchAlgorithmException SHA1"); } md.reset(); md.update(password.getBytes()); byteHash = md.digest(); for (int i = 0; i < byteHash.length; i++) { resultString.append(Integer.toHexString(0xFF & byteHash[i])); } return (resultString.toString()); } | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | 885,750 |
0 | @Deprecated public void test() { try { String query = "* <http://xmlns.com/foaf/0.1/workplaceHomepage> <http://www.deri.ie/>" + "* <http://xmlns.com/foaf/0.1/knows> *"; String url = "http://sindice.com/api/v2/search?qt=advanced&q=" + URLEncoder.encode(query, "utf-8") + "&qt=advanced"; URL urlObj = new URL(url); URLConnection con = urlObj.openConnection(); if (con != null) { Model model = ModelFactory.createDefaultModel(); model.read(con.getInputStream(), null); } System.out.println(url); } catch (MalformedURLException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } | public void parseFile(String dataurl, URL documentBase) { DataInputStream in; if (_debug > 2) System.out.println("PlotBox: parseFile(" + dataurl + " " + documentBase + ") _dataurl = " + _dataurl + " " + _documentBase); if (dataurl == null || dataurl.length() == 0) { in = new DataInputStream(System.in); } else { try { URL url; if (documentBase == null && _documentBase != null) { documentBase = _documentBase; } if (documentBase == null) { url = new URL(_dataurl); } else { try { url = new URL(documentBase, dataurl); } catch (NullPointerException e) { url = new URL(_dataurl); } } in = new DataInputStream(url.openStream()); } catch (MalformedURLException e) { try { in = new DataInputStream(new FileInputStream(dataurl)); } catch (FileNotFoundException me) { _errorMsg = new String[2]; _errorMsg[0] = "File not found: " + dataurl; _errorMsg[1] = me.getMessage(); return; } catch (SecurityException me) { _errorMsg = new String[2]; _errorMsg[0] = "Security Exception: " + dataurl; _errorMsg[1] = me.getMessage(); return; } } catch (IOException ioe) { _errorMsg = new String[2]; _errorMsg[0] = "Failure opening URL: " + dataurl; _errorMsg[1] = ioe.getMessage(); return; } } _newFile(); try { if (_binary) { _parseBinaryStream(in); } else { String line = in.readLine(); while (line != null) { _parseLine(line); line = in.readLine(); } } } catch (MalformedURLException e) { _errorMsg = new String[2]; _errorMsg[0] = "Malformed URL: " + dataurl; _errorMsg[1] = e.getMessage(); return; } catch (IOException e) { _errorMsg = new String[2]; _errorMsg[0] = "Failure reading data: " + dataurl; _errorMsg[1] = e.getMessage(); } catch (PlotDataException e) { _errorMsg = new String[2]; _errorMsg[0] = "Incorrectly formatted plot data in " + dataurl; _errorMsg[1] = e.getMessage(); } finally { try { in.close(); } catch (IOException me) { } } } | 885,751 |
0 | public Object run() { if (type == GET_THEME_DIR) { String sep = File.separator; String[] dirs = new String[] { userHome + sep + ".themes", System.getProperty("swing.metacitythemedir"), "/usr/share/themes", "/usr/gnome/share/themes", "/opt/gnome2/share/themes" }; URL themeDir = null; for (int i = 0; i < dirs.length; i++) { if (dirs[i] == null) { continue; } File dir = new File(dirs[i] + sep + arg + sep + "metacity-1"); if (new File(dir, "metacity-theme-1.xml").canRead()) { try { themeDir = dir.toURL(); } catch (MalformedURLException ex) { themeDir = null; } break; } } if (themeDir == null) { String filename = "resources/metacity/" + arg + "/metacity-1/metacity-theme-1.xml"; URL url = getClass().getResource(filename); if (url != null) { String str = url.toString(); try { themeDir = new URL(str.substring(0, str.lastIndexOf('/')) + "/"); } catch (MalformedURLException ex) { themeDir = null; } } } return themeDir; } else if (type == GET_USER_THEME) { try { userHome = System.getProperty("user.home"); String theme = System.getProperty("swing.metacitythemename"); if (theme != null) { return theme; } URL url = new URL(new File(userHome).toURL(), ".gconf/apps/metacity/general/%25gconf.xml"); Reader reader = new InputStreamReader(url.openStream(), "ISO-8859-1"); char[] buf = new char[1024]; StringBuffer strBuf = new StringBuffer(); int n; while ((n = reader.read(buf)) >= 0) { strBuf.append(buf, 0, n); } reader.close(); String str = strBuf.toString(); if (str != null) { String strLowerCase = str.toLowerCase(); int i = strLowerCase.indexOf("<entry name=\"theme\""); if (i >= 0) { i = strLowerCase.indexOf("<stringvalue>", i); if (i > 0) { i += "<stringvalue>".length(); int i2 = str.indexOf("<", i); return str.substring(i, i2); } } } } catch (MalformedURLException ex) { } catch (IOException ex) { } return null; } else if (type == GET_IMAGE) { return new ImageIcon((URL) arg).getImage(); } else { return null; } } | @SuppressWarnings("unchecked") public HttpResponse putFile(String root, String to_path, File file_obj) throws DropboxException { String path = "/files/" + root + to_path; try { Path targetPath = new Path(path); String target = buildFullURL(secureProtocol, content_host, port, buildURL(targetPath.removeLastSegments(1).addTrailingSeparator().toString(), API_VERSION, null)); HttpClient client = getClient(target); HttpPost req = new HttpPost(target); List nvps = new ArrayList(); nvps.add(new BasicNameValuePair("file", targetPath.lastSegment())); req.setEntity(new UrlEncodedFormEntity(nvps, HTTP.UTF_8)); auth.sign(req); MultipartEntity entity = new MultipartEntity(HttpMultipartMode.BROWSER_COMPATIBLE); FileBody bin = new FileBody(file_obj, targetPath.lastSegment(), "application/octet-stream", null); entity.addPart("file", bin); req.setEntity(entity); HttpResponse resp = client.execute(req); resp.getEntity().consumeContent(); return resp; } catch (Exception e) { throw new DropboxException(e); } } | 885,752 |
0 | public void insertStringInFile(String file, String textToInsert, long fromByte, long toByte) throws Exception { String tmpFile = file + ".tmp"; BufferedInputStream in = null; BufferedOutputStream out = null; long byteCount = 0; try { in = new BufferedInputStream(new FileInputStream(new File(file))); out = new BufferedOutputStream(new FileOutputStream(tmpFile)); long size = fromByte; byte[] buf = null; if (size == 0) { } else { buf = new byte[(int) size]; int length = -1; if ((length = in.read(buf)) != -1) { out.write(buf, 0, length); byteCount = byteCount + length; } else { String msg = "Failed to read the first '" + size + "' bytes of file '" + file + "'. This might be a programming error."; logger.warning(msg); throw new Exception(msg); } } buf = textToInsert.getBytes(); int length = buf.length; out.write(buf, 0, length); byteCount = byteCount + length; long skipLength = toByte - fromByte; long skippedBytes = in.skip(skipLength); if (skippedBytes == -1) { } else { buf = new byte[4096]; length = -1; while ((length = in.read(buf)) != -1) { out.write(buf, 0, length); byteCount = byteCount + length; } } in.close(); in = null; out.close(); out = null; File fileToDelete = new File(file); boolean wasDeleted = fileToDelete.delete(); if (!wasDeleted) { String msg = "Failed to delete the original file '" + file + "' to replace it with the modified file after text insertion."; logger.warning(msg); throw new Exception(msg); } File fileToRename = new File(tmpFile); boolean wasRenamed = fileToRename.renameTo(fileToDelete); if (!wasRenamed) { String msg = "Failed to rename tmp file '" + tmpFile + "' to the name of the original file '" + file + "'"; logger.warning(msg); throw new Exception(msg); } } catch (Exception e) { logger.log(Level.WARNING, "Failed to read/write file '" + file + "'.", e); throw e; } finally { if (in != null) { try { in.close(); } catch (IOException e) { logger.log(Level.FINEST, "Ignoring error closing input file '" + file + "'.", e); } } if (out != null) { try { out.close(); } catch (IOException e) { logger.log(Level.FINEST, "Ignoring error closing output file '" + tmpFile + "'.", e); } } } } | private void sortMasters() { masterCounter = 0; for (int i = 0; i < maxID; i++) { if (users[i].getMasterPoints() > 0) { masterHandleList[masterCounter] = users[i].getHandle(); masterPointsList[masterCounter] = users[i].getMasterPoints(); masterCounter = masterCounter + 1; } } for (int i = masterCounter; --i >= 0; ) { for (int j = 0; j < i; j++) { if (masterPointsList[j] > masterPointsList[j + 1]) { int tempp = masterPointsList[j]; String temppstring = masterHandleList[j]; masterPointsList[j] = masterPointsList[j + 1]; masterHandleList[j] = masterHandleList[j + 1]; masterPointsList[j + 1] = tempp; masterHandleList[j + 1] = temppstring; } } } } | 885,753 |
1 | public void setUp() { configureProject("src/etc/testcases/taskdefs/optional/net/ftp.xml"); getProject().executeTarget("setup"); tmpDir = getProject().getProperty("tmp.dir"); ftp = new FTPClient(); ftpFileSep = getProject().getProperty("ftp.filesep"); myFTPTask.setSeparator(ftpFileSep); myFTPTask.setProject(getProject()); remoteTmpDir = myFTPTask.resolveFile(tmpDir); String remoteHost = getProject().getProperty("ftp.host"); int port = Integer.parseInt(getProject().getProperty("ftp.port")); String remoteUser = getProject().getProperty("ftp.user"); String password = getProject().getProperty("ftp.password"); try { ftp.connect(remoteHost, port); } catch (Exception ex) { connectionSucceeded = false; loginSuceeded = false; System.out.println("could not connect to host " + remoteHost + " on port " + port); } if (connectionSucceeded) { try { ftp.login(remoteUser, password); } catch (IOException ioe) { loginSuceeded = false; System.out.println("could not log on to " + remoteHost + " as user " + remoteUser); } } } | private static void ftpTest() { FTPClient f = new FTPClient(); try { f.connect("oscomak.net"); System.out.print(f.getReplyString()); f.setFileType(FTPClient.BINARY_FILE_TYPE); } catch (SocketException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } String password = JOptionPane.showInputDialog("Enter password"); if (password == null || password.equals("")) { System.out.println("No password"); return; } try { f.login("oscomak_pointrel", password); System.out.print(f.getReplyString()); } catch (IOException e) { e.printStackTrace(); } try { String workingDirectory = f.printWorkingDirectory(); System.out.println("Working directory: " + workingDirectory); System.out.print(f.getReplyString()); } catch (IOException e1) { e1.printStackTrace(); } try { f.enterLocalPassiveMode(); System.out.print(f.getReplyString()); System.out.println("Trying to list files"); String[] fileNames = f.listNames(); System.out.print(f.getReplyString()); System.out.println("Got file list fileNames: " + fileNames.length); for (String fileName : fileNames) { System.out.println("File: " + fileName); } System.out.println(); System.out.println("done reading stream"); System.out.println("trying alterative way to read stream"); ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); f.retrieveFile(fileNames[0], outputStream); System.out.println("size: " + outputStream.size()); System.out.println(outputStream.toString()); System.out.println("done with alternative"); System.out.println("Trying to store file back"); ByteArrayInputStream inputStream = new ByteArrayInputStream(outputStream.toByteArray()); boolean storeResult = f.storeFile("test.txt", inputStream); System.out.println("Done storing " + storeResult); f.disconnect(); System.out.print(f.getReplyString()); System.out.println("disconnected"); } catch (IOException e) { e.printStackTrace(); } } | 885,754 |
1 | public static void main(String[] args) { paraProc(args); CanonicalGFF cgff = new CanonicalGFF(gffFilename); CanonicalGFF geneModel = new CanonicalGFF(modelFilename); CanonicalGFF transcriptGff = new CanonicalGFF(transcriptFilename); TreeMap ksTable1 = getKsTable(ksTable1Filename); TreeMap ksTable2 = getKsTable(ksTable2Filename); Map intronReadCntMap = new TreeMap(); Map intronSplicingPosMap = new TreeMap(); try { BufferedReader fr = new BufferedReader(new FileReader(inFilename)); while (fr.ready()) { String line = fr.readLine(); if (line.startsWith("#")) continue; String tokens[] = line.split("\t"); String chr = tokens[0]; int start = Integer.parseInt(tokens[1]); int stop = Integer.parseInt(tokens[2]); GenomeInterval intron = new GenomeInterval(chr, start, stop); int readCnt = Integer.parseInt(tokens[3]); intronReadCntMap.put(intron, readCnt); String splicingMapStr = tokens[4]; Map splicingMap = getSplicingMap(splicingMapStr); intronSplicingPosMap.put(intron, splicingMap); } fr.close(); } catch (IOException ex) { ex.printStackTrace(); System.exit(1); } double[] hdCDF = getHdCdf(readLength, minimumOverlap); try { FileWriter fw = new FileWriter(outFilename); for (Iterator intronIterator = intronReadCntMap.keySet().iterator(); intronIterator.hasNext(); ) { GenomeInterval intron = (GenomeInterval) intronIterator.next(); int readCnt = ((Integer) intronReadCntMap.get(intron)).intValue(); TreeMap splicingMap = (TreeMap) intronSplicingPosMap.get(intron); Object ksInfoArray[] = distributionAccepter((TreeMap) splicingMap.clone(), readCnt, hdCDF, ksTable1, ksTable2); boolean ksAccepted = (Boolean) ksInfoArray[0]; double testK = (Double) ksInfoArray[1]; double standardK1 = (Double) ksInfoArray[2]; double standardK2 = (Double) ksInfoArray[3]; int positionCnt = splicingMap.size(); Object modelInfoArray[] = getModelAgreedSiteCnt(intron, cgff, geneModel, transcriptGff); int modelAgreedSiteCnt = (Integer) modelInfoArray[0]; int maxAgreedTransSiteCnt = (Integer) modelInfoArray[1]; boolean containedBySomeGene = (Boolean) modelInfoArray[2]; int numIntersectingGenes = (Integer) modelInfoArray[3]; int distance = intron.getStop() - intron.getStart(); fw.write(intron.getChr() + ":" + intron.getStart() + ".." + intron.getStop() + "\t" + distance + "\t" + readCnt + "\t" + splicingMap + "\t" + probabilityEvaluation(readLength, distance, readCnt, splicingMap, positionCnt) + "\t" + ksAccepted + "\t" + testK + "\t" + standardK1 + "\t" + standardK2 + "\t" + positionCnt + "\t" + modelAgreedSiteCnt + "\t" + maxAgreedTransSiteCnt + "\t" + containedBySomeGene + "\t" + numIntersectingGenes + "\n"); } fw.close(); } catch (IOException ex) { ex.printStackTrace(); System.exit(1); } } | public static void translateTableMetaData(String baseDir, String tableName, NameSpaceDefinition nsDefinition) throws Exception { setVosiNS(baseDir, "table", nsDefinition); String filename = baseDir + "table.xsl"; Scanner s = new Scanner(new File(filename)); PrintWriter fw = new PrintWriter(new File(baseDir + tableName + ".xsl")); while (s.hasNextLine()) { fw.println(s.nextLine().replaceAll("TABLENAME", tableName)); } s.close(); fw.close(); applyStyle(baseDir + "tables.xml", baseDir + tableName + ".json", baseDir + tableName + ".xsl"); } | 885,755 |
1 | private boolean copy_to_file_io(File src, File dst) throws IOException { InputStream is = null; OutputStream os = null; try { is = new FileInputStream(src); is = new BufferedInputStream(is); os = new FileOutputStream(dst); os = new BufferedOutputStream(os); byte buffer[] = new byte[1024 * 64]; int read; while ((read = is.read(buffer)) > 0) { os.write(buffer, 0, read); } return true; } finally { try { if (is != null) is.close(); } catch (IOException e) { Debug.debug(e); } try { if (os != null) os.close(); } catch (IOException e) { Debug.debug(e); } } } | public static boolean copyFile(File from, File tu) { final int BUFFER_SIZE = 4096; byte[] buffer = new byte[BUFFER_SIZE]; try { FileInputStream in = new FileInputStream(from); FileOutputStream out = new FileOutputStream(tu); int read; while ((read = in.read(buffer)) != -1) { out.write(buffer, 0, read); } in.close(); out.close(); } catch (IOException e) { return false; } return true; } | 885,756 |
0 | protected static DynamicJasperDesign generateJasperDesign(DynamicReport dr) throws CoreException { DynamicJasperDesign jd = null; try { if (dr.getTemplateFileName() != null) { log.info("loading template file: " + dr.getTemplateFileName()); log.info("Attemping to find the file directly in the file system..."); File file = new File(dr.getTemplateFileName()); if (file.exists()) { JasperDesign jdesign = JRXmlLoader.load(file); jd = DJJRDesignHelper.downCast(jdesign, dr); } else { log.info("Not found: Attemping to find the file in the classpath..."); URL url = DynamicJasperHelper.class.getClassLoader().getResource(dr.getTemplateFileName()); JasperDesign jdesign = JRXmlLoader.load(url.openStream()); jd = DJJRDesignHelper.downCast(jdesign, dr); } JasperDesignHelper.populateReportOptionsFromDesign(jd, dr); } else { jd = DJJRDesignHelper.getNewDesign(dr); } registerParameters(jd, dr); } catch (JRException e) { throw new CoreException(e.getMessage(), e); } catch (IOException e) { throw new CoreException(e.getMessage(), e); } return jd; } | public static List<Item> doService(List<String> itemIds, Boolean archive) throws UnsupportedEncodingException, IOException { DefaultHttpClient httpclient = new DefaultHttpClient(); ToggleArchiveRequest request = new ToggleArchiveRequest(); String sessionId = (String) RuntimeAccess.getInstance().getSession().getAttribute("SESSION_ID"); request.setItemIds(itemIds); request.setArchive(archive); request.setSessionId(sessionId); XStream writer = new XStream(); writer.setMode(XStream.XPATH_ABSOLUTE_REFERENCES); writer.alias("ToggleArchiveRequest", ToggleArchiveRequest.class); XStream reader = new XStream(); reader.setMode(XStream.XPATH_ABSOLUTE_REFERENCES); reader.alias("ToggleArchiveResponse", ToggleArchiveResponse.class); String strRequest = URLEncoder.encode(reader.toXML(request), "UTF-8"); HttpPost httppost = new HttpPost(MewitProperties.getMewitUrl() + "/resources/toggleArchive?REQUEST=" + strRequest); HttpResponse response = httpclient.execute(httppost); HttpEntity entity = response.getEntity(); if (entity != null) { String result = URLDecoder.decode(EntityUtils.toString(entity), "UTF-8"); ToggleArchiveResponse oResponse = (ToggleArchiveResponse) reader.fromXML(result); return oResponse.getItems(); } return null; } | 885,757 |
1 | public static void extract(final File destDir, final Collection<ZipEntryInfo> entryInfos) throws IOException { if (destDir == null || CollectionUtils.isEmpty(entryInfos)) throw new IllegalArgumentException("One or parameter is null or empty!"); if (!destDir.exists()) destDir.mkdirs(); for (ZipEntryInfo entryInfo : entryInfos) { ZipEntry entry = entryInfo.getZipEntry(); InputStream in = entryInfo.getInputStream(); File entryDest = new File(destDir, entry.getName()); entryDest.getParentFile().mkdirs(); if (!entry.isDirectory()) { OutputStream out = new FileOutputStream(new File(destDir, entry.getName())); try { IOUtils.copy(in, out); out.flush(); } finally { IOUtils.closeQuietly(in); IOUtils.closeQuietly(out); } } } } | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | 885,758 |
0 | public static File downloadFile(Proxy proxy, URL url, File path) throws IOException { URLConnection conn = null; if (null == proxy) { conn = url.openConnection(); } else { conn = url.openConnection(proxy); } conn.connect(); File destFile = null; if (conn instanceof HttpURLConnection) { HttpURLConnection hc = (HttpURLConnection) conn; String filename = null; String hv = hc.getHeaderField("Content-Disposition"); if (null == hv) { String str = url.toString(); int index = str.lastIndexOf("/"); filename = str.substring(index + 1); } else { int index = hv.indexOf("filename="); filename = hv.substring(index).replace("\"", "").trim(); } destFile = new File(path, filename); } else { destFile = new File(path, "downloadfile" + url.toString().hashCode()); } if (destFile.exists()) { return destFile; } FileOutputStream fos = new FileOutputStream(destFile); byte[] buffer = new byte[2048]; try { while (true) { int len = conn.getInputStream().read(buffer); if (len < 0) { break; } else { fos.write(buffer, 0, len); } } fos.close(); } catch (IOException e) { destFile.delete(); throw e; } return destFile; } | public static String remove_file(String sessionid, String key) { String resultJsonString = "some problem existed inside the create_new_tag() function if you see this string"; try { Log.d("current running function name:", "remove_file"); HttpClient httpclient = new DefaultHttpClient(); HttpPost httppost = new HttpPost("https://mt0-app.cloud.cm/rpc/json"); List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(2); nameValuePairs.add(new BasicNameValuePair("c", "Storage")); nameValuePairs.add(new BasicNameValuePair("m", "remove_file")); nameValuePairs.add(new BasicNameValuePair("keys", key)); httppost.setEntity(new UrlEncodedFormEntity(nameValuePairs)); httppost.setHeader("Cookie", "PHPSESSID=" + sessionid); HttpResponse response = httpclient.execute(httppost); resultJsonString = EntityUtils.toString(response.getEntity()); Log.d("jsonStringReturned:", resultJsonString); return resultJsonString; } catch (Exception e) { e.printStackTrace(); } return resultJsonString; } | 885,759 |
0 | private final String encryptPassword(String pass) { MessageDigest md = null; try { md = MessageDigest.getInstance("SHA-1"); } catch (NoSuchAlgorithmException e) { log.log(Level.WARNING, "Error while obtaining decript algorithm", e); throw new RuntimeException("AccountData.encryptPassword()"); } try { md.update(pass.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { log.log(Level.WARNING, "Problem with decript algorithm occured.", e); throw new RuntimeException("AccountData.encryptPassword()"); } return new BASE64Encoder().encode(md.digest()); } | public ObservationResult[] call(String url, String servicename, String srsname, String version, String offering, String observed_property, String responseFormat) { System.out.println("GetObservationBasic.call url " + url); URL service = null; URLConnection connection = null; ArrayList<ObservationResult> obsList = new ArrayList<ObservationResult>(); boolean isDataArrayRead = false; try { service = new URL(url); connection = service.openConnection(); } catch (MalformedURLException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } connection.setDoOutput(true); connection.setDoInput(true); connection.setUseCaches(false); connection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); try { DataOutputStream out = new DataOutputStream(connection.getOutputStream()); GetObservationDocument getobDoc = GetObservationDocument.Factory.newInstance(); GetObservation getob = getobDoc.addNewGetObservation(); getob.setService(servicename); getob.setVersion(version); getob.setSrsName(srsname); getob.setOffering(offering); getob.setObservedPropertyArray(new String[] { observed_property }); getob.setResponseFormat(responseFormat); String request = URLEncoder.encode(getobDoc.xmlText(), "UTF-8"); out.writeBytes(request); out.flush(); out.close(); } catch (UnsupportedEncodingException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } try { URL observation_url = new URL("file:///E:/Temp/Observation.xml"); URLConnection urlc = observation_url.openConnection(); urlc.connect(); InputStream observation_url_is = urlc.getInputStream(); ObservationCollectionDocument obsCollDoc = ObservationCollectionDocument.Factory.parse(observation_url_is); ObservationCollectionType obsColl = obsCollDoc.getObservationCollection(); ObservationPropertyType[] aObsPropType = obsColl.getMemberArray(); for (ObservationPropertyType observationPropertyType : aObsPropType) { ObservationType observation = observationPropertyType.getObservation(); if (observation != null) { System.out.println("observation " + observation.getClass().getName()); ObservationResult obsResult = new ObservationResult(); if (observation instanceof GeometryObservationTypeImpl) { GeometryObservationTypeImpl geometryObservation = (GeometryObservationTypeImpl) observation; TimeObjectPropertyType samplingTime = geometryObservation.getSamplingTime(); TimeInstantTypeImpl timeInstant = (TimeInstantTypeImpl) samplingTime.getTimeObject(); TimePositionType timePosition = timeInstant.getTimePosition(); String time = (String) timePosition.getObjectValue(); StringTokenizer date_st; String day = new StringTokenizer(time, "T").nextToken(); SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); Date d = sdf.parse(day); String timetemp = null; date_st = new StringTokenizer(time, "T"); while (date_st.hasMoreElements()) timetemp = date_st.nextToken(); sdf = new SimpleDateFormat("HH:mm:ss"); Date ti = sdf.parse(timetemp.substring(0, timetemp.lastIndexOf(':') + 2)); d.setHours(ti.getHours()); d.setMinutes(ti.getMinutes()); d.setSeconds(ti.getSeconds()); obsResult.setDatetime(d); String textValue = "null"; FeaturePropertyType featureOfInterest = (FeaturePropertyType) geometryObservation.getFeatureOfInterest(); Node fnode = featureOfInterest.getDomNode(); NodeList childNodes = fnode.getChildNodes(); for (int j = 0; j < childNodes.getLength(); j++) { Node cnode = childNodes.item(j); if (cnode.getNodeName().equals("n52:movingObject")) { NamedNodeMap att = cnode.getAttributes(); Node id = att.getNamedItem("gml:id"); textValue = id.getNodeValue(); obsResult.setTextValue(textValue); obsResult.setIsTextValue(true); } } XmlObject result = geometryObservation.getResult(); if (result instanceof GeometryPropertyTypeImpl) { GeometryPropertyTypeImpl geometryPropertyType = (GeometryPropertyTypeImpl) result; AbstractGeometryType geometry = geometryPropertyType.getGeometry(); String srsName = geometry.getSrsName(); StringTokenizer st = new StringTokenizer(srsName, ":"); String epsg = null; while (st.hasMoreElements()) epsg = st.nextToken(); int sri = Integer.parseInt(epsg); if (geometry instanceof PointTypeImpl) { PointTypeImpl point = (PointTypeImpl) geometry; Node node = point.getDomNode(); PointDocument pointDocument = PointDocument.Factory.parse(node); PointType point2 = pointDocument.getPoint(); XmlCursor cursor = point.newCursor(); cursor.toFirstChild(); CoordinatesDocument coordinatesDocument = CoordinatesDocument.Factory.parse(cursor.xmlText()); CoordinatesType coords = coordinatesDocument.getCoordinates(); StringTokenizer tok = new StringTokenizer(coords.getStringValue(), " ,;", false); double x = Double.parseDouble(tok.nextToken()); double y = Double.parseDouble(tok.nextToken()); double z = 0; if (tok.hasMoreTokens()) { z = Double.parseDouble(tok.nextToken()); } x += 207561; y += 3318814; z += 20; Point3d center = new Point3d(x, y, z); obsResult.setCenter(center); GeometryFactory fact = new GeometryFactory(); Coordinate coordinate = new Coordinate(x, y, z); Geometry g1 = fact.createPoint(coordinate); g1.setSRID(sri); obsResult.setGeometry(g1); String href = observation.getProcedure().getHref(); obsResult.setProcedure(href); obsList.add(obsResult); } } } } } observation_url_is.close(); } catch (IOException e) { e.printStackTrace(); } catch (XmlException e) { e.printStackTrace(); } catch (Exception e) { e.printStackTrace(); } ObservationResult[] ar = new ObservationResult[obsList.size()]; return obsList.toArray(ar); } | 885,760 |
1 | protected List<Datastream> getDatastreams(final DepositCollection pDeposit) throws IOException, SWORDException { List<Datastream> tDatastreams = new ArrayList<Datastream>(); LOG.debug("copying file"); String tZipTempFileName = super.getTempDir() + "uploaded-file.tmp"; IOUtils.copy(pDeposit.getFile(), new FileOutputStream(tZipTempFileName)); Datastream tDatastream = new LocalDatastream(super.getGenericFileName(pDeposit), this.getContentType(), tZipTempFileName); tDatastreams.add(tDatastream); tDatastreams.addAll(_zipFile.getFiles(tZipTempFileName)); return tDatastreams; } | public void run() { LogPrinter.log(Level.FINEST, "Started Download at : {0, date, long}", new Date()); if (!PipeConnected) { throw new IllegalStateException("You should connect the pipe before with getInputStream()"); } InputStream ins = null; if (IsAlreadyDownloaded) { LogPrinter.log(Level.FINEST, "The file already Exists open and foward the byte"); try { ContentLength = (int) TheAskedFile.length(); ContentType = URLConnection.getFileNameMap().getContentTypeFor(TheAskedFile.getName()); ins = new FileInputStream(TheAskedFile); byte[] buffer = new byte[BUFFER_SIZE]; int read = ins.read(buffer); while (read >= 0) { Pipe.write(buffer, 0, read); read = ins.read(buffer); } } catch (IOException e) { e.printStackTrace(); } finally { if (ins != null) { try { ins.close(); } catch (IOException e) { } } } } else { LogPrinter.log(Level.FINEST, "the file does not exist locally so we try to download the thing"); File theDir = TheAskedFile.getParentFile(); if (!theDir.exists()) { theDir.mkdirs(); } for (URL url : ListFastest) { FileOutputStream fout = null; boolean OnError = false; long timestart = System.currentTimeMillis(); long bytecount = 0; try { URL newUrl = new URL(url.toString() + RequestedFile); LogPrinter.log(Level.FINEST, "the download URL = {0}", newUrl); URLConnection conn = newUrl.openConnection(); ContentType = conn.getContentType(); ContentLength = conn.getContentLength(); ins = conn.getInputStream(); fout = new FileOutputStream(TheAskedFile); byte[] buffer = new byte[BUFFER_SIZE]; int read = ins.read(buffer); while (read >= 0) { fout.write(buffer, 0, read); Pipe.write(buffer, 0, read); read = ins.read(buffer); bytecount += read; } Pipe.flush(); } catch (IOException e) { OnError = true; } finally { if (ins != null) { try { ins.close(); } catch (IOException e) { } } if (fout != null) { try { fout.close(); } catch (IOException e) { } } } long timeend = System.currentTimeMillis(); if (OnError) { continue; } else { long timetook = timeend - timestart; BigDecimal speed = new BigDecimal(bytecount).multiply(new BigDecimal(1000)).divide(new BigDecimal(timetook), MathContext.DECIMAL32); for (ReportCalculatedStatistique report : Listener) { report.reportUrlStat(url, speed, timetook); } break; } } } LogPrinter.log(Level.FINEST, "download finished at {0,date,long}", new Date()); if (Pipe != null) { try { Pipe.close(); } catch (IOException e) { e.printStackTrace(); } } } | 885,761 |
1 | protected static final void copyFile(String from, String to) throws SeleniumException { try { java.io.File fileFrom = new File(from); java.io.File fileTo = new File(to); FileReader in = new FileReader(fileFrom); FileWriter out = new FileWriter(fileTo); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (Exception e) { throw new SeleniumException("Failed to copy new file : " + from + " to : " + to, e); } } | protected Object openDialogBox(Control cellEditorWindow) { FileDialog dialog = new FileDialog(parent.getShell(), SWT.OPEN); dialog.setFilterExtensions(new String[] { "*.jpg;*.JPG;*.JPEG;*.gif;*.GIF;*.png;*.PNG", "*.jpg;*.JPG;*.JPEG", "*.gif;*.GIF", "*.png;*.PNG" }); dialog.setFilterNames(new String[] { "All", "Joint Photographic Experts Group (JPEG)", "Graphics Interchange Format (GIF)", "Portable Network Graphics (PNG)" }); String imagePath = dialog.open(); if (imagePath == null) return null; IProject project = ProjectManager.getInstance().getCurrentProject(); String projectFolderPath = project.getLocation().toOSString(); File imageFile = new File(imagePath); String fileName = imageFile.getName(); ImageData imageData = null; try { imageData = new ImageData(imagePath); } catch (SWTException e) { UserErrorException error = new UserErrorException(PropertyHandler.getInstance().getProperty("_invalid_image_title"), PropertyHandler.getInstance().getProperty("_invalid_image_text")); UserErrorService.INSTANCE.showError(error); return null; } if (imageData == null) { UserErrorException error = new UserErrorException(PropertyHandler.getInstance().getProperty("_invalid_image_title"), PropertyHandler.getInstance().getProperty("_invalid_image_text")); UserErrorService.INSTANCE.showError(error); return null; } File copiedImageFile = new File(projectFolderPath + File.separator + imageFolderPath + File.separator + fileName); if (copiedImageFile.exists()) { Path path = new Path(copiedImageFile.getPath()); copiedImageFile = new File(projectFolderPath + File.separator + imageFolderPath + File.separator + UUID.randomUUID().toString() + "." + path.getFileExtension()); } try { copiedImageFile.createNewFile(); } catch (IOException e1) { ExceptionHandlingService.INSTANCE.handleException(e1); copiedImageFile = null; } if (copiedImageFile == null) { copiedImageFile = new File(projectFolderPath + File.separator + imageFolderPath + File.separator + UUID.randomUUID().toString()); try { copiedImageFile.createNewFile(); } catch (IOException e) { ExceptionHandlingService.INSTANCE.handleException(e); return ""; } } FileReader in = null; FileWriter out = null; try { in = new FileReader(imageFile); out = new FileWriter(copiedImageFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (FileNotFoundException e) { ExceptionHandlingService.INSTANCE.handleException(e); return ""; } catch (IOException e) { ExceptionHandlingService.INSTANCE.handleException(e); return ""; } return imageFolderPath + File.separator + copiedImageFile.getName(); } | 885,762 |
1 | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | public static boolean buildCFItem2ItemStats(String outFileName, String movieAvgFileName, String custAvgFileName) { try { File infile = new File(completePath + fSep + "SmartGRAPE" + fSep + movieAvgFileName); FileChannel inC = new FileInputStream(infile).getChannel(); int size = (int) inC.size(); ByteBuffer map = inC.map(FileChannel.MapMode.READ_ONLY, 0, size); TShortFloatHashMap movieAverages = new TShortFloatHashMap(17770, 1); inC.close(); while (map.hasRemaining()) { movieAverages.put(map.getShort(), map.getFloat()); } map = null; infile = new File(completePath + fSep + "SmartGRAPE" + fSep + custAvgFileName); inC = new FileInputStream(infile).getChannel(); size = (int) inC.size(); map = inC.map(FileChannel.MapMode.READ_ONLY, 0, size); TIntFloatHashMap custAverages = new TIntFloatHashMap(480189, 1); inC.close(); while (map.hasRemaining()) { custAverages.put(map.getInt(), map.getFloat()); } File outfile = new File(completePath + fSep + "SmartGRAPE" + fSep + outFileName); FileChannel outC = new FileOutputStream(outfile, true).getChannel(); short[] movies = CustomersAndRatingsPerMovie.keys(); Arrays.sort(movies); int noMovies = movies.length; for (int i = 0; i < noMovies - 1; i++) { short movie1 = movies[i]; TIntByteHashMap testMovieCustAndRatingsMap = (TIntByteHashMap) CustomersAndRatingsPerMovie.get(movie1); int[] customers1 = testMovieCustAndRatingsMap.keys(); Arrays.sort(customers1); System.out.println("Processing movie: " + movie1); for (int j = i + 1; j < noMovies; j++) { short movie2 = movies[j]; TIntByteHashMap otherMovieCustAndRatingsMap = (TIntByteHashMap) CustomersAndRatingsPerMovie.get(movie2); int[] customers2 = otherMovieCustAndRatingsMap.keys(); TIntArrayList intersectSet = CustOverLapForTwoMoviesCustom(customers1, customers2); int count = 0; float diffRating = 0; float pearsonCorr = 0; float cosineCorr = 0; float adjustedCosineCorr = 0; float sumX = 0; float sumY = 0; float sumXY = 0; float sumX2 = 0; float sumY2 = 0; float sumXYPearson = 0; float sumX2Pearson = 0; float sumY2Pearson = 0; float sumXYACos = 0; float sumX2ACos = 0; float sumY2ACos = 0; if ((intersectSet.size() == 0) || (intersectSet == null)) { count = 0; diffRating = 0; } else { count = intersectSet.size(); for (int l = 0; l < count; l++) { int commonCust = intersectSet.getQuick(l); byte ratingX = testMovieCustAndRatingsMap.get(commonCust); sumX += ratingX; byte ratingY = otherMovieCustAndRatingsMap.get(commonCust); sumY += ratingY; sumX2 += ratingX * ratingX; sumY2 += ratingY * ratingY; sumXY += ratingX * ratingY; diffRating += ratingX - ratingY; sumXYPearson += (ratingX - movieAverages.get(movie1)) * (ratingY - movieAverages.get(movie2)); sumX2Pearson += Math.pow((ratingX - movieAverages.get(movie1)), 2); sumY2Pearson += Math.pow((ratingY - movieAverages.get(movie2)), 2); float custAverage = custAverages.get(commonCust); sumXYACos += (ratingX - custAverage) * (ratingY - custAverage); sumX2ACos += Math.pow((ratingX - custAverage), 2); sumY2ACos += Math.pow((ratingY - custAverage), 2); } } double pearsonDenominator = Math.sqrt(sumX2Pearson) * Math.sqrt(sumY2Pearson); if (pearsonDenominator == 0.0) { pearsonCorr = 0; } else { pearsonCorr = new Double(sumXYPearson / pearsonDenominator).floatValue(); } double adjCosineDenominator = Math.sqrt(sumX2ACos) * Math.sqrt(sumY2ACos); if (adjCosineDenominator == 0.0) { adjustedCosineCorr = 0; } else { adjustedCosineCorr = new Double(sumXYACos / adjCosineDenominator).floatValue(); } double cosineDenominator = Math.sqrt(sumX2) * Math.sqrt(sumY2); if (cosineDenominator == 0.0) { cosineCorr = 0; } else { cosineCorr = new Double(sumXY / cosineDenominator).floatValue(); } ByteBuffer buf = ByteBuffer.allocate(44); buf.putShort(movie1); buf.putShort(movie2); buf.putInt(count); buf.putFloat(diffRating); buf.putFloat(sumXY); buf.putFloat(sumX); buf.putFloat(sumY); buf.putFloat(sumX2); buf.putFloat(sumY2); buf.putFloat(pearsonCorr); buf.putFloat(adjustedCosineCorr); buf.putFloat(cosineCorr); buf.flip(); outC.write(buf); buf.clear(); } } outC.close(); return true; } catch (Exception e) { e.printStackTrace(); return false; } } | 885,763 |
0 | public static String httpUrlConnection_post(String targetURL, String urlParameters) { System.out.println("httpUrlConnection_post"); URL url; HttpURLConnection connection = null; try { url = new URL(targetURL); connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("POST"); connection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); connection.setRequestProperty("Content-Length", "" + Integer.toString(urlParameters.getBytes().length)); connection.setRequestProperty("Content-Language", "en-US"); connection.setUseCaches(false); connection.setConnectTimeout(5000); connection.setReadTimeout(5000); connection.setDoInput(true); connection.setDoOutput(true); DataOutputStream wr = new DataOutputStream(connection.getOutputStream()); wr.writeBytes(urlParameters); wr.flush(); wr.close(); InputStream is = connection.getInputStream(); BufferedReader rd = new BufferedReader(new InputStreamReader(is)); String line; StringBuilder response = new StringBuilder(); while ((line = rd.readLine()) != null) { response.append(line); response.append('\r'); } rd.close(); return response.toString(); } catch (Exception e) { System.out.print(e); return null; } finally { if (connection != null) { connection.disconnect(); } } } | private void makeDailyBackup() throws CacheOperationException, ConfigurationException { final int MAX_DAILY_BACKUPS = 5; File cacheFolder = getBackupFolder(); cacheLog.debug("Making a daily backup of current Beehive archive..."); try { File oldestDaily = new File(DAILY_BACKUP_PREFIX + "." + MAX_DAILY_BACKUPS); if (oldestDaily.exists()) { moveToWeeklyBackup(oldestDaily); } for (int index = MAX_DAILY_BACKUPS - 1; index > 0; index--) { File daily = new File(cacheFolder, DAILY_BACKUP_PREFIX + "." + index); File target = new File(cacheFolder, DAILY_BACKUP_PREFIX + "." + (index + 1)); if (!daily.exists()) { cacheLog.debug("Daily backup file ''{0}'' was not present. Skipping...", daily.getAbsolutePath()); continue; } if (!daily.renameTo(target)) { sortBackups(); throw new CacheOperationException("There was an error moving ''{0}'' to ''{1}''.", daily.getAbsolutePath(), target.getAbsolutePath()); } else { cacheLog.debug("Moved " + daily.getAbsolutePath() + " to " + target.getAbsolutePath()); } } } catch (SecurityException e) { throw new ConfigurationException("Security Manager has denied read/write access to daily backup files in ''{0}'' : {1}" + e, cacheFolder.getAbsolutePath(), e.getMessage()); } File beehiveArchive = getCachedArchive(); File tempBackupArchive = new File(cacheFolder, BEEHIVE_ARCHIVE_NAME + ".tmp"); BufferedInputStream archiveReader = null; BufferedOutputStream tempBackupWriter = null; try { archiveReader = new BufferedInputStream(new FileInputStream(beehiveArchive)); tempBackupWriter = new BufferedOutputStream(new FileOutputStream(tempBackupArchive)); int len, bytecount = 0; final int BUFFER_SIZE = 4096; byte[] buffer = new byte[BUFFER_SIZE]; while ((len = archiveReader.read(buffer, 0, BUFFER_SIZE)) != -1) { tempBackupWriter.write(buffer, 0, len); bytecount += len; } tempBackupWriter.flush(); long originalFileSize = beehiveArchive.length(); if (originalFileSize != bytecount) { throw new CacheOperationException("Original archive size was {0} bytes but only {1} were copied.", originalFileSize, bytecount); } cacheLog.debug("Finished copying ''{0}'' to ''{1}''.", beehiveArchive.getAbsolutePath(), tempBackupArchive.getAbsolutePath()); } catch (FileNotFoundException e) { throw new CacheOperationException("Files required for copying a backup of Beehive archive could not be found, opened " + "or created : {1}", e, e.getMessage()); } catch (IOException e) { throw new CacheOperationException("Error while making a copy of the Beehive archive : {0}", e, e.getMessage()); } finally { if (archiveReader != null) { try { archiveReader.close(); } catch (Throwable t) { cacheLog.warn("Failed to close stream to ''{0}'' : {1}", t, beehiveArchive.getAbsolutePath(), t.getMessage()); } } if (tempBackupWriter != null) { try { tempBackupWriter.close(); } catch (Throwable t) { cacheLog.warn("Failed to close stream to ''{0}'' : {1}", t, tempBackupArchive.getAbsolutePath(), t.getMessage()); } } } validateArchive(tempBackupArchive); File newestDaily = getNewestDailyBackupFile(); try { if (!tempBackupArchive.renameTo(newestDaily)) { throw new CacheOperationException("Error moving ''{0}'' to ''{1}''.", tempBackupArchive.getAbsolutePath(), newestDaily.getAbsolutePath()); } else { cacheLog.info("Backup complete. Saved in ''{0}''", newestDaily.getAbsolutePath()); } } catch (SecurityException e) { throw new ConfigurationException("Security Manager has denied write access to ''{0}'' : {1}", e, newestDaily.getAbsolutePath(), e.getMessage()); } } | 885,764 |
1 | private void processHelpFile() { InputStream in = null; if (line.hasOption("helpfile")) { OutputStream out = null; try { String filename = line.getOptionValue("helpfile"); in = new FileInputStream(filename); filename = filename.replace('\\', '/'); filename = filename.substring(filename.lastIndexOf('/') + 1); File outFile = new File(outputDir, filename); if (LOG.isInfoEnabled()) { LOG.info("Processing generated file " + outFile.getAbsolutePath()); } out = new FileOutputStream(outFile); baseProperties.setProperty("helpfile", filename); IOUtils.copy(in, out); } catch (FileNotFoundException e) { LOG.error(e.getMessage(), e); } catch (IOException e) { LOG.error(e.getMessage(), e); } finally { if (in != null) { try { in.close(); } catch (IOException e) { LOG.error(e.getMessage(), e); } } if (out != null) { try { out.close(); } catch (IOException e) { LOG.error(e.getMessage(), e); } } } return; } Properties props = new Properties(baseProperties); ClassLoader cl = this.getClass().getClassLoader(); Document doc = null; try { in = cl.getResourceAsStream(RESOURCE_PKG + "/help-doc.xml"); doc = XmlUtils.parse(in); } catch (XmlException e) { LOG.error(e.getMessage(), e); } finally { if (in != null) { try { in.close(); } catch (IOException e) { LOG.error(e.getMessage(), e); } } } transformResource(doc, "help-doc.xsl", props, "help-doc.html"); baseProperties.setProperty("helpfile", "help-doc.html"); } | @Test public void testWriteAndReadBiggerUnbuffered() throws Exception { JCFSFileServer server = new JCFSFileServer(defaultTcpPort, defaultTcpAddress, defaultUdpPort, defaultUdpAddress, dir, 0, 0); JCFS.configureDiscovery(defaultUdpAddress, defaultUdpPort); try { server.start(); RFile file = new RFile("testreadwriteb.txt"); RFileOutputStream out = new RFileOutputStream(file); String body = ""; int size = 50 * 1024; for (int i = 0; i < size; i++) { body = body + "a"; } out.write(body.getBytes("utf-8")); out.close(); File expected = new File(dir, "testreadwriteb.txt"); assertTrue(expected.isFile()); assertEquals(body.length(), expected.length()); RFileInputStream in = new RFileInputStream(file); ByteArrayOutputStream tmp = new ByteArrayOutputStream(); int b = in.read(); while (b != -1) { tmp.write(b); b = in.read(); } byte[] buffer = tmp.toByteArray(); in.close(); assertEquals(body.length(), buffer.length); String resultRead = new String(buffer, "utf-8"); assertEquals(body, resultRead); } finally { server.stop(); } } | 885,765 |
0 | String getOutputPage(String action, String XML, String xslFileName, InputStream pageS, HttpServletRequest request) throws NoSuchAlgorithmException, UnsupportedEncodingException, TransformerException { String sPage = null; Transformer transformer = null; String dig = null; CharArrayWriter page = new CharArrayWriter(); if (this.nCachedPages > 0) { java.security.MessageDigest mess = java.security.MessageDigest.getInstance("SHA1"); mess.update(XML.getBytes()); mess.update(Long.toString(new File(basePath + xslFileName).lastModified()).getBytes()); dig = new String(mess.digest()); synchronized (pages) { if (pages.containsKey(dig)) { sPage = pages.get(dig); } } } if (sPage == null && xslFileName.length() > 4) { try { long modifyTime = new File(basePath + xslFileName).lastModified(); String path = basePath.replaceAll("\\\\", "/") + xslFileName; path = "file:///" + path; boolean add2cache = false; if (this.nCachedTransformers > 0) { String cacheKey = action + xslFileName + modifyTime; if (this.transformers.containsKey(cacheKey)) { transformer = this.transformers.get(cacheKey); synchronized (transformer) { transformer.transform(new StreamSource(new ByteArrayInputStream(XML.getBytes("UTF-8"))), new StreamResult(page)); } } else { add2cache = true; } } if (transformer == null) { transformer = TransformerFactory.newInstance().newTransformer(new StreamSource(path)); transformer.transform(new StreamSource(new ByteArrayInputStream(XML.getBytes("UTF-8"))), new StreamResult(page)); } sPage = page.toString(); sPage = sPage.replaceAll("<", "<"); sPage = sPage.replaceAll(">", ">"); sPage = replaceLinks(sPage, request); if (this.nCachedPages > 0) { synchronized (pages) { pages.put(dig, sPage); if (pages.size() > nCachedPages) { Iterator<String> i = pages.values().iterator(); i.next(); i.remove(); } } } if (add2cache) { synchronized (this.transformers) { this.transformers.put(action + xslFileName + modifyTime, transformer); if (this.transformers.size() > this.nCachedTransformers) { Iterator<Transformer> it = this.transformers.values().iterator(); it.next(); it.remove(); } } } } catch (TransformerException ex) { Logger.getLogger(getClass().getName()).log(Level.SEVERE, "---------------------------------------------"); Logger.getLogger(getClass().getName()).log(Level.SEVERE, null, ex); Logger.getLogger(getClass().getName()).log(Level.SEVERE, ("XSL file: " + xslFileName)); Logger.getLogger(getClass().getName()).log(Level.SEVERE, XML); Logger.getLogger(getClass().getName()).log(Level.SEVERE, "---------------------------------------------"); throw ex; } } return sPage; } | private void displayDiffResults() throws IOException { File outFile = File.createTempFile("diff", ".htm"); outFile.deleteOnExit(); FileOutputStream outStream = new FileOutputStream(outFile); BufferedWriter out = new BufferedWriter(new OutputStreamWriter(outStream)); out.write("<html><head><title>LOC Differences</title>\n" + SCRIPT + "</head>\n" + "<body bgcolor='#ffffff'>\n" + "<div onMouseOver=\"window.defaultStatus='Metrics'\">\n"); if (addedTable.length() > 0) { out.write("<table border><tr><th>Files Added:</th>" + "<th>Add</th><th>Type</th></tr>"); out.write(addedTable.toString()); out.write("</table><br><br>"); } if (modifiedTable.length() > 0) { out.write("<table border><tr><th>Files Modified:</th>" + "<th>Base</th><th>Del</th><th>Mod</th><th>Add</th>" + "<th>Total</th><th>Type</th></tr>"); out.write(modifiedTable.toString()); out.write("</table><br><br>"); } if (deletedTable.length() > 0) { out.write("<table border><tr><th>Files Deleted:</th>" + "<th>Del</th><th>Type</th></tr>"); out.write(deletedTable.toString()); out.write("</table><br><br>"); } out.write("<table name=METRICS BORDER>\n"); if (modifiedTable.length() > 0 || deletedTable.length() > 0) { out.write("<tr><td>Base: </td><td>"); out.write(Long.toString(base)); out.write("</td></tr>\n<tr><td>Deleted: </td><td>"); out.write(Long.toString(deleted)); out.write("</td></tr>\n<tr><td>Modified: </td><td>"); out.write(Long.toString(modified)); out.write("</td></tr>\n<tr><td>Added: </td><td>"); out.write(Long.toString(added)); out.write("</td></tr>\n<tr><td>New & Changed: </td><td>"); out.write(Long.toString(added + modified)); out.write("</td></tr>\n"); } out.write("<tr><td>Total: </td><td>"); out.write(Long.toString(total)); out.write("</td></tr>\n</table></div>"); redlinesOut.close(); out.flush(); InputStream redlines = new FileInputStream(redlinesTempFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = redlines.read(buffer)) != -1) outStream.write(buffer, 0, bytesRead); outStream.write("</BODY></HTML>".getBytes()); outStream.close(); Browser.launch(outFile.toURL().toString()); } | 885,766 |
1 | public static void copyFile(File src, File dest) throws IOException { log.debug("Copying file: '" + src + "' to '" + dest + "'"); FileChannel srcChannel = new FileInputStream(src).getChannel(); FileChannel dstChannel = new FileOutputStream(dest).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } | public File createFileFromClasspathResource(String resourceUrl) throws IOException { File fichierTest = File.createTempFile("xmlFieldTestFile", ""); FileOutputStream fos = new FileOutputStream(fichierTest); InputStream is = DefaultXmlFieldSelectorTest.class.getResourceAsStream(resourceUrl); IOUtils.copy(is, fos); is.close(); fos.close(); return fichierTest; } | 885,767 |
0 | private static void main(String[] args) { try { File f = new File("test.txt"); if (f.exists()) { throw new IOException(f + " already exists. I don't want to overwrite it."); } StraightStreamReader in; char[] cbuf = new char[0x1000]; int read; int totRead; FileOutputStream out = new FileOutputStream(f); for (int i = 0x00; i < 0x100; i++) { out.write(i); } out.close(); in = new StraightStreamReader(new FileInputStream(f)); for (int i = 0x00; i < 0x100; i++) { read = in.read(); if (read != i) { System.err.println("Error: " + i + " read as " + read); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = in.read(cbuf); if (totRead != 0x100) { System.err.println("Simple buffered read did not read the full amount: 0x" + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead, 0x100 - totRead)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead + 0x123, 0x100 - totRead)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i + 0x123] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i + 0x123]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead + 0x123, 7)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i + 0x123] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i + 0x123]); } } in.close(); f.delete(); } catch (IOException x) { System.err.println(x.getMessage()); } } | public static InputStream openStream(URL url) { try { URLConnection connection = url.openConnection(); connection.setUseCaches(false); return connection.getInputStream(); } catch (IOException e) { throw new IORuntimeException(e); } } | 885,768 |
1 | public static String computeMD5(InputStream input) { InputStream digestStream = null; try { MessageDigest md5 = MessageDigest.getInstance("MD5"); digestStream = new DigestInputStream(input, md5); IOUtils.copy(digestStream, new NullOutputStream()); return new String(Base64.encodeBase64(md5.digest()), "UTF-8"); } catch (NoSuchAlgorithmException e) { throw new RuntimeException(e); } catch (IOException e) { throw new RuntimeException(e); } finally { IOUtils.closeQuietly(digestStream); } } | protected String encrypt(final String data, final String key) throws CryptographicFailureException { Validate.notNull(data, "Provided data cannot be null."); Validate.notNull(key, "Provided key name cannot be null."); final PublicKey pk = getPublicKey(key); if (pk == null) { throw new CryptographicFailureException("PublicKeyNotFound", String.format("Cannot find public key '%s'", key)); } try { final Cipher cipher = Cipher.getInstance(pk.getAlgorithm()); cipher.init(Cipher.ENCRYPT_MODE, pk); final ByteArrayInputStream bin = new ByteArrayInputStream(data.getBytes()); final CipherInputStream cin = new CipherInputStream(bin, cipher); final ByteArrayOutputStream bout = new ByteArrayOutputStream(); IOUtils.copy(cin, bout); return new String(Base64.encodeBase64(bout.toByteArray())); } catch (NoSuchAlgorithmException e) { throw new IllegalStateException(String.format("Cannot find instance of algorithm '%s'", pk.getAlgorithm()), e); } catch (NoSuchPaddingException e) { throw new IllegalStateException(String.format("Cannot build instance of algorithm '%s'", pk.getAlgorithm()), e); } catch (InvalidKeyException e) { throw new IllegalStateException(String.format("Cannot build instance of algorithm '%s'", pk.getAlgorithm()), e); } catch (IOException e) { throw new IllegalStateException("Cannot build in-memory cipher copy", e); } } | 885,769 |
1 | public void putFile(CompoundName file, FileInputStream fileInput) throws IOException { File fullDir = new File(REMOTE_BASE_DIR.getCanonicalPath()); for (int i = 0; i < file.size() - 1; i++) fullDir = new File(fullDir, file.get(i)); fullDir.mkdirs(); File outputFile = new File(fullDir, file.get(file.size() - 1)); FileOutputStream outStream = new FileOutputStream(outputFile); for (int byteIn = fileInput.read(); byteIn != -1; byteIn = fileInput.read()) outStream.write(byteIn); fileInput.close(); outStream.close(); } | private void displayDiffResults() throws IOException { File outFile = File.createTempFile("diff", ".htm"); outFile.deleteOnExit(); FileOutputStream outStream = new FileOutputStream(outFile); BufferedWriter out = new BufferedWriter(new OutputStreamWriter(outStream)); out.write("<html><head><title>LOC Differences</title>\n" + SCRIPT + "</head>\n" + "<body bgcolor='#ffffff'>\n" + "<div onMouseOver=\"window.defaultStatus='Metrics'\">\n"); if (addedTable.length() > 0) { out.write("<table border><tr><th>Files Added:</th>" + "<th>Add</th><th>Type</th></tr>"); out.write(addedTable.toString()); out.write("</table><br><br>"); } if (modifiedTable.length() > 0) { out.write("<table border><tr><th>Files Modified:</th>" + "<th>Base</th><th>Del</th><th>Mod</th><th>Add</th>" + "<th>Total</th><th>Type</th></tr>"); out.write(modifiedTable.toString()); out.write("</table><br><br>"); } if (deletedTable.length() > 0) { out.write("<table border><tr><th>Files Deleted:</th>" + "<th>Del</th><th>Type</th></tr>"); out.write(deletedTable.toString()); out.write("</table><br><br>"); } out.write("<table name=METRICS BORDER>\n"); if (modifiedTable.length() > 0 || deletedTable.length() > 0) { out.write("<tr><td>Base: </td><td>"); out.write(Long.toString(base)); out.write("</td></tr>\n<tr><td>Deleted: </td><td>"); out.write(Long.toString(deleted)); out.write("</td></tr>\n<tr><td>Modified: </td><td>"); out.write(Long.toString(modified)); out.write("</td></tr>\n<tr><td>Added: </td><td>"); out.write(Long.toString(added)); out.write("</td></tr>\n<tr><td>New & Changed: </td><td>"); out.write(Long.toString(added + modified)); out.write("</td></tr>\n"); } out.write("<tr><td>Total: </td><td>"); out.write(Long.toString(total)); out.write("</td></tr>\n</table></div>"); redlinesOut.close(); out.flush(); InputStream redlines = new FileInputStream(redlinesTempFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = redlines.read(buffer)) != -1) outStream.write(buffer, 0, bytesRead); outStream.write("</BODY></HTML>".getBytes()); outStream.close(); Browser.launch(outFile.toURL().toString()); } | 885,770 |
0 | protected void downgradeHistory(Collection<String> versions) { Assert.notEmpty(versions); try { Connection connection = this.database.getDefaultConnection(); PreparedStatement statement = connection.prepareStatement("UPDATE " + this.logTableName + " SET RESULT = 'DOWNGRADED' WHERE TYPE = 'B' AND TARGET = ? AND RESULT = 'COMPLETE'"); boolean commit = false; try { for (String version : versions) { statement.setString(1, version); int modified = statement.executeUpdate(); Assert.isTrue(modified <= 1, "Expecting not more than 1 record to be updated, not " + modified); } commit = true; } finally { statement.close(); if (commit) connection.commit(); else connection.rollback(); } } catch (SQLException e) { throw new SystemException(e); } } | @Override public boolean checkConnection() { int status = 0; try { URL url = new URL(TupeloProxy.endpoint); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); status = conn.getResponseCode(); } catch (Exception e) { logger.severe("Connection test failed with code:" + status); e.printStackTrace(); } if (status < 200 || status >= 400) return false; String url = this.url + "?title=Special:UserLogin&action=submitlogin&type=login&returnto=Main_Page&wpDomain=" + domain + "&wpLoginattempt=Log%20in&wpName=" + username + "&wpPassword=" + password; return true; } | 885,771 |
0 | public static void unzip(File sourceZipFile, File unzipDestinationDirectory, FileFilter filter) throws IOException { unzipDestinationDirectory.mkdirs(); if (!unzipDestinationDirectory.exists()) { throw new IOException("Unable to create destination directory: " + unzipDestinationDirectory); } ZipFile zipFile; zipFile = new ZipFile(sourceZipFile, ZipFile.OPEN_READ); Enumeration<? extends ZipEntry> zipFileEntries = zipFile.entries(); while (zipFileEntries.hasMoreElements()) { ZipEntry entry = (ZipEntry) zipFileEntries.nextElement(); if (!entry.isDirectory()) { String currentEntry = entry.getName(); File destFile = new File(unzipDestinationDirectory, currentEntry); if (filter == null || filter.accept(destFile)) { File destinationParent = destFile.getParentFile(); destinationParent.mkdirs(); BufferedInputStream is = new BufferedInputStream(zipFile.getInputStream(entry)); FileOutputStream fos = new FileOutputStream(destFile); IOUtils.copyLarge(is, fos); fos.flush(); IOUtils.closeQuietly(fos); } } } zipFile.close(); } | public byte[] getDigest(OMText text, String digestAlgorithm) throws OMException { byte[] digest = new byte[0]; try { MessageDigest md = MessageDigest.getInstance(digestAlgorithm); md.update((byte) 0); md.update((byte) 0); md.update((byte) 0); md.update((byte) 3); md.update(text.getText().getBytes("UnicodeBigUnmarked")); digest = md.digest(); } catch (NoSuchAlgorithmException e) { throw new OMException(e); } catch (UnsupportedEncodingException e) { throw new OMException(e); } return digest; } | 885,772 |
1 | private void displayDiffResults() throws IOException { File outFile = File.createTempFile("diff", ".htm"); outFile.deleteOnExit(); FileOutputStream outStream = new FileOutputStream(outFile); BufferedWriter out = new BufferedWriter(new OutputStreamWriter(outStream)); out.write("<html><head><title>LOC Differences</title>\n" + SCRIPT + "</head>\n" + "<body bgcolor='#ffffff'>\n" + "<div onMouseOver=\"window.defaultStatus='Metrics'\">\n"); if (addedTable.length() > 0) { out.write("<table border><tr><th>Files Added:</th>" + "<th>Add</th><th>Type</th></tr>"); out.write(addedTable.toString()); out.write("</table><br><br>"); } if (modifiedTable.length() > 0) { out.write("<table border><tr><th>Files Modified:</th>" + "<th>Base</th><th>Del</th><th>Mod</th><th>Add</th>" + "<th>Total</th><th>Type</th></tr>"); out.write(modifiedTable.toString()); out.write("</table><br><br>"); } if (deletedTable.length() > 0) { out.write("<table border><tr><th>Files Deleted:</th>" + "<th>Del</th><th>Type</th></tr>"); out.write(deletedTable.toString()); out.write("</table><br><br>"); } out.write("<table name=METRICS BORDER>\n"); if (modifiedTable.length() > 0 || deletedTable.length() > 0) { out.write("<tr><td>Base: </td><td>"); out.write(Long.toString(base)); out.write("</td></tr>\n<tr><td>Deleted: </td><td>"); out.write(Long.toString(deleted)); out.write("</td></tr>\n<tr><td>Modified: </td><td>"); out.write(Long.toString(modified)); out.write("</td></tr>\n<tr><td>Added: </td><td>"); out.write(Long.toString(added)); out.write("</td></tr>\n<tr><td>New & Changed: </td><td>"); out.write(Long.toString(added + modified)); out.write("</td></tr>\n"); } out.write("<tr><td>Total: </td><td>"); out.write(Long.toString(total)); out.write("</td></tr>\n</table></div>"); redlinesOut.close(); out.flush(); InputStream redlines = new FileInputStream(redlinesTempFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = redlines.read(buffer)) != -1) outStream.write(buffer, 0, bytesRead); outStream.write("</BODY></HTML>".getBytes()); outStream.close(); Browser.launch(outFile.toURL().toString()); } | private static boolean hardCopy(File sourceFile, File destinationFile, StringBuffer errorLog) { boolean result = true; try { notifyCopyStart(destinationFile); destinationFile.getParentFile().mkdirs(); byte[] buffer = new byte[4096]; int len = 0; FileInputStream in = new FileInputStream(sourceFile); FileOutputStream out = new FileOutputStream(destinationFile); while ((len = in.read(buffer)) != -1) out.write(buffer, 0, len); in.close(); out.close(); } catch (Exception e) { result = false; handleException("\n Error in method: copy!\n", e, errorLog); } finally { notifyCopyEnd(destinationFile); } return result; } | 885,773 |
1 | public MapInfo loadLocalMapData(String fileName) { MapInfo info = mapCacheLocal.get(fileName); if (info != null && info.getContent() == null) { try { BufferedReader bufferedreader; URL fetchUrl = new URL(localMapContextUrl, fileName); URLConnection urlconnection = fetchUrl.openConnection(); if (urlconnection.getContentEncoding() != null) { bufferedreader = new BufferedReader(new InputStreamReader(urlconnection.getInputStream(), urlconnection.getContentEncoding())); } else { bufferedreader = new BufferedReader(new InputStreamReader(urlconnection.getInputStream(), "utf-8")); } String line; StringBuilder mapContent = new StringBuilder(); while ((line = bufferedreader.readLine()) != null) { mapContent.append(line); mapContent.append("\n"); } info.setContent(mapContent.toString()); GameMapImplementation gameMap = GameMapImplementation.createFromMapInfo(info); } catch (IOException _ex) { System.err.println("HexTD::readFile:: Can't read from " + fileName); } } else { System.err.println("HexTD::readFile:: file not in cache: " + fileName); } return info; } | public static void doVersionCheck(View view) { view.showWaitCursor(); try { URL url = new URL(jEdit.getProperty("version-check.url")); InputStream in = url.openStream(); BufferedReader bin = new BufferedReader(new InputStreamReader(in)); String line; String develBuild = null; String stableBuild = null; while ((line = bin.readLine()) != null) { if (line.startsWith(".build")) develBuild = line.substring(6).trim(); else if (line.startsWith(".stablebuild")) stableBuild = line.substring(12).trim(); } bin.close(); if (develBuild != null && stableBuild != null) { doVersionCheck(view, stableBuild, develBuild); } } catch (IOException e) { String[] args = { jEdit.getProperty("version-check.url"), e.toString() }; GUIUtilities.error(view, "read-error", args); } view.hideWaitCursor(); } | 885,774 |
0 | public void copy(String pathFileIn, String pathFileOut) { try { File inputFile = new File(pathFileIn); File outputFile = new File(pathFileOut); FileReader in = new FileReader(inputFile); File outDir = new File(DirOut); if (!outDir.exists()) outDir.mkdirs(); FileWriter out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); this.printColumn(inputFile.getName(), outputFile.getPath()); } catch (Exception e) { e.printStackTrace(); } } | public void fetchCourses(String jsonurl) { if (jsonurl == null) { throw new NullPointerException("jsonurl"); } InputStreamReader in = null; try { URL url = new URL(jsonurl); in = new InputStreamReader(url.openConnection().getInputStream()); JSONObject root = (JSONObject) JSONValue.parse(in); JSONArray courseAr = (JSONArray) root.get("courses"); ListIterator<JSONObject> it = courseAr.listIterator(); SimpleDateFormat df = new SimpleDateFormat("yyyy-MM-dd"); while (it.hasNext()) { JSONObject obj = it.next(); Course c; try { c = new Course((String) obj.get("course"), df.parse((String) obj.get("start_date")), df.parse((String) obj.get("end_date"))); courses.add(c); } catch (ParseException pe) { } } in.close(); } catch (IOException e) { } finally { if (in != null) { try { in.close(); } catch (IOException e) { } } } } | 885,775 |
1 | private void getRandomGUID(boolean secure) { MessageDigest md5 = null; StringBuffer sbValueBeforeMD5 = new StringBuffer(); try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { System.out.println("Error: " + e); } try { long time = System.currentTimeMillis(); long rand = 0; if (secure) { rand = mySecureRand.nextLong(); } else { rand = myRand.nextLong(); } sbValueBeforeMD5.append(s_id); sbValueBeforeMD5.append(":"); sbValueBeforeMD5.append(Long.toString(time)); sbValueBeforeMD5.append(":"); sbValueBeforeMD5.append(Long.toString(rand)); valueBeforeMD5 = sbValueBeforeMD5.toString(); md5.update(valueBeforeMD5.getBytes()); byte[] array = md5.digest(); StringBuffer sb = new StringBuffer(); for (int j = 0; j < array.length; ++j) { int b = array[j] & 0xFF; if (b < 0x10) sb.append('0'); sb.append(Integer.toHexString(b)); } valueAfterMD5 = sb.toString(); } catch (Exception e) { System.out.println("Error:" + e); } } | public void createMd5Hash() { try { String vcardObject = new ContactToVcard(TimeZone.getTimeZone("UTC"), "UTF-8").convert(this); MessageDigest m = MessageDigest.getInstance("MD5"); m.update(vcardObject.getBytes()); this.md5Hash = new BigInteger(m.digest()).toString(); if (log.isTraceEnabled()) { log.trace("Hash is:" + this.md5Hash); } } catch (ConverterException ex) { log.error("Error creating hash:" + ex.getMessage()); } catch (NoSuchAlgorithmException noSuchAlgorithmException) { log.error("Error creating hash:" + noSuchAlgorithmException.getMessage()); } } | 885,776 |
1 | public int procesar() { int mas = 0; String uriOntologia = "", source = "", uri = ""; String fichOrigenHTML = "", fichOrigenLN = ""; String ficheroOutOWL = ""; md5 firma = null; StringTokenV2 entra = null, entra2 = null, entra3 = null; FileInputStream lengNat = null; BufferedInputStream lengNat2 = null; DataInputStream entradaLenguajeNatural = null; FileWriter salOWL = null; BufferedWriter salOWL2 = null; PrintWriter salidaOWL = null; String sujeto = "", verbo = "", CD = "", CI = "", fraseOrigen = ""; StringTokenV2 token2; boolean bandera = false; OntClass c = null; OntClass cBak = null; String claseTrabajo = ""; String nombreClase = "", nombrePropiedad = "", variasPalabras = ""; int incre = 0, emergencia = 0; String lineaSalida = ""; String[] ontologia = new String[5]; ontologia[0] = "http://www.criado.info/owl/vertebrados_es.owl#"; ontologia[1] = "http://www.w3.org/2001/sw/WebOnt/guide-src/wine#"; ontologia[2] = "http://www.co-ode.org/ontologies/pizza/2005/10/18/pizza.owl#"; ontologia[3] = "http://www.w3.org/2001/sw/WebOnt/guide-src/food#"; ontologia[4] = "http://www.daml.org/2001/01/gedcom/gedcom#"; String[] ontologiaSource = new String[5]; ontologiaSource[0] = this.directorioMapeo + "\\" + "mapeo_vertebrados_es.xml"; ontologiaSource[1] = this.directorioMapeo + "\\" + "mapeo_wine_es.xml"; ontologiaSource[2] = this.directorioMapeo + "\\" + "mapeo_pizza_es.xml"; ontologiaSource[3] = this.directorioMapeo + "\\" + "mapeo_food_es.xml"; ontologiaSource[4] = this.directorioMapeo + "\\" + "mapeo_parentesco_es.xml"; mapeoIdiomas clasesOntologias; try { if ((entrada = entradaFichero.readLine()) != null) { if (entrada.trim().length() > 10) { entrada2 = new StringTokenV2(entrada.trim(), "\""); if (entrada2.isIncluidaSubcadena("<fichero ontologia=")) { ontologiaOrigen = entrada2.getToken(2); fichOrigenHTML = entrada2.getToken(4); fichOrigenLN = entrada2.getToken(6); if (ontologiaOrigen.equals("VERTEBRADOS")) { source = ontologiaSource[0]; uriOntologia = ontologia[0]; } if (ontologiaOrigen.equals("WINE")) { source = ontologiaSource[1]; uriOntologia = ontologia[1]; } if (ontologiaOrigen.equals("PIZZA")) { source = ontologiaSource[2]; uriOntologia = ontologia[2]; } if (ontologiaOrigen.equals("FOOD")) { source = ontologiaSource[3]; uriOntologia = ontologia[3]; } if (ontologiaOrigen.equals("PARENTESCOS")) { source = ontologiaSource[4]; uriOntologia = ontologia[4]; } firma = new md5(uriOntologia, false); clasesOntologias = new mapeoIdiomas(source); uri = ""; ficheroOutOWL = ""; entra2 = new StringTokenV2(fichOrigenHTML, "\\"); int numToken = entra2.getNumeroTokenTotales(); entra = new StringTokenV2(fichOrigenHTML, " "); if (entra.isIncluidaSubcadena(directorioLocal)) { entra = new StringTokenV2(entra.getQuitar(directorioLocal) + "", " "); uri = entra.getCambiar("\\", "/"); uri = entra.getQuitar(entra2.getToken(numToken)) + ""; entra3 = new StringTokenV2(entra2.getToken(numToken), "."); ficheroOutOWL = entra3.getToken(1) + "_" + firma.toString() + ".owl"; uri = urlPatron + uri + ficheroOutOWL; } entra3 = new StringTokenV2(fichOrigenHTML, "."); ficheroOutOWL = entra3.getToken(1) + "_" + firma.toString() + ".owl"; lineaSalida = "<vistasemantica origen=\"" + fichOrigenLN + "\" destino=\"" + uri + "\" />"; lengNat = new FileInputStream(fichOrigenLN); lengNat2 = new BufferedInputStream(lengNat); entradaLenguajeNatural = new DataInputStream(lengNat2); salOWL = new FileWriter(ficheroOutOWL); salOWL2 = new BufferedWriter(salOWL); salidaOWL = new PrintWriter(salOWL2); while ((entradaInstancias = entradaLenguajeNatural.readLine()) != null) { sujeto = ""; verbo = ""; CD = ""; CI = ""; fraseOrigen = ""; if (entradaInstancias.trim().length() > 10) { entrada2 = new StringTokenV2(entradaInstancias.trim(), "\""); if (entrada2.isIncluidaSubcadena("<oracion sujeto=")) { sujeto = entrada2.getToken(2).trim(); verbo = entrada2.getToken(4).trim(); CD = entrada2.getToken(6).trim(); CI = entrada2.getToken(8).trim(); fraseOrigen = entrada2.getToken(10).trim(); if (sujeto.length() > 0 & verbo.length() > 0 & CD.length() > 0) { bandera = false; c = null; cBak = null; nombreClase = clasesOntologias.getClaseInstancia(CD); if (nombreClase.length() > 0) { bandera = true; } if (bandera) { if (incre == 0) { salidaOWL.write(" <rdf:RDF " + "\n"); salidaOWL.write(" xmlns:j.0=\"" + uriOntologia + "\"" + "\n"); salidaOWL.write(" xmlns:protege=\"http://protege.stanford.edu/plugins/owl/protege#\"" + "\n"); salidaOWL.write(" xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"" + "\n"); salidaOWL.write(" xmlns:xsd=\"http://www.w3.org/2001/XMLSchema#\"" + "\n"); salidaOWL.write(" xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\"" + "\n"); salidaOWL.write(" xmlns:owl=\"http://www.w3.org/2002/07/owl#\" " + "\n"); salidaOWL.write(" xmlns=\"" + uri + "#\"" + "\n"); salidaOWL.write(" xml:base=\"" + uri + "\">" + "\n"); salidaOWL.write(" <owl:Ontology rdf:about=\"\">" + "\n"); salidaOWL.write(" <owl:imports rdf:resource=\"" + uriOntologia + "\"/>" + "\n"); salidaOWL.write(" </owl:Ontology>" + "\n"); salidaOWL.flush(); salida.write(lineaSalida + "\n"); salida.flush(); incre = 1; } salidaOWL.write(" <j.0:" + nombreClase + " rdf:ID=\"" + sujeto.toUpperCase() + "\"/>" + "\n"); salidaOWL.write(" <owl:AllDifferent>" + "\n"); salidaOWL.write(" <owl:distinctMembers rdf:parseType=\"Collection\">" + "\n"); salidaOWL.write(" <" + nombreClase + " rdf:about=\"#" + sujeto.toUpperCase() + "\"/>" + "\n"); salidaOWL.write(" </owl:distinctMembers>" + "\n"); salidaOWL.write(" </owl:AllDifferent>" + "\n"); salidaOWL.flush(); bandera = false; } } } } } salidaOWL.write(" </rdf:RDF>" + "\n" + "\n"); salidaOWL.write("<!-- Creado por [html2ws] http://www.luis.criado.org -->" + "\n"); salidaOWL.flush(); } } mas = 1; } else { salida.write("</listaVistasSemanticas>\n"); salida.flush(); salida.close(); bw2.close(); fw2.close(); salidaOWL.close(); entradaFichero.close(); ent2.close(); ent1.close(); mas = -1; } } catch (Exception e) { mas = -2; salida.write("No se encuentra: " + fichOrigen + "\n"); salida.flush(); } return mas; } | public static File writeInternalFile(Context cx, URL url, String dir, String filename) { FileOutputStream fos = null; File fi = null; try { fi = newInternalFile(cx, dir, filename); fos = FileUtils.openOutputStream(fi); int length = IOUtils.copy(url.openStream(), fos); log(length + " bytes copyed."); } catch (IOException e) { AIOUtils.log("", e); } finally { try { fos.close(); } catch (IOException e) { AIOUtils.log("", e); } } return fi; } | 885,777 |
0 | public void load(String fileName) { BufferedReader bufReader; loaded = false; vector.removeAllElements(); try { if (fileName.startsWith("http:")) { URL url = new URL(fileName); bufReader = new BufferedReader(new InputStreamReader(url.openStream())); } else bufReader = new BufferedReader(new FileReader(fileName)); String inputLine; while ((inputLine = bufReader.readLine()) != null) { if (listener != null) listener.handleLine(inputLine); else vector.add(inputLine); } bufReader.close(); loaded = true; } catch (IOException e) { errorMsg = e.getMessage(); } } | public static void copyFile(File src, File dst) throws IOException { File inputFile = src; File outputFile = dst; FileReader in = new FileReader(inputFile); FileWriter out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } | 885,778 |
0 | private void copyTemplates(ProjectPath pPath) { String sourceAntPath = pPath.sourceAntPath(); final String moduleName = projectOperations.getFocusedTopLevelPackage().toString(); logger.info("Module Name: " + moduleName); String targetDirectory = pPath.canonicalFileSystemPath(projectOperations); logger.info("Moving into target Directory: " + targetDirectory); if (!targetDirectory.endsWith("/")) { targetDirectory += "/"; } if (!fileManager.exists(targetDirectory)) { fileManager.createDirectory(targetDirectory); } System.out.println("Target Directory: " + pPath.sourceAntPath()); String path = TemplateUtils.getTemplatePath(getClass(), sourceAntPath); Set<URL> urls = UrlFindingUtils.findMatchingClasspathResources(context.getBundleContext(), path); Assert.notNull(urls, "Could not search bundles for resources for Ant Path '" + path + "'"); if (urls.isEmpty()) { logger.info("URLS are empty stopping..."); } for (URL url : urls) { logger.info("Stepping into " + url.toExternalForm()); String fileName = url.getPath().substring(url.getPath().lastIndexOf("/") + 1); fileName = fileName.replace("-template", ""); String targetFilename = targetDirectory + fileName; logger.info("Handling " + targetFilename); if (!fileManager.exists(targetFilename)) { try { logger.info("Copied file"); String input = FileCopyUtils.copyToString(new InputStreamReader(url.openStream())); logger.info("TopLevelPackage: " + projectOperations.getFocusedTopLevelPackage()); logger.info("SegmentPackage: " + pPath.canonicalFileSystemPath(projectOperations)); String topLevelPackage = projectOperations.getFocusedTopLevelPackage().toString(); input = input.replace("__TOP_LEVEL_PACKAGE__", topLevelPackage); input = input.replace("__SEGMENT_PACKAGE__", pPath.segmentPackage()); input = input.replace("__PROJECT_NAME__", projectOperations.getFocusedProjectName()); input = input.replace("__ENTITY_NAME__", entityName); MutableFile mutableFile = fileManager.createFile(targetFilename); FileCopyUtils.copy(input.getBytes(), mutableFile.getOutputStream()); } catch (IOException ioe) { throw new IllegalStateException("Unable to create '" + targetFilename + "'", ioe); } } } } | public void xtestFile2() throws Exception { InputStream inputStream = new FileInputStream(IOTest.FILE); OutputStream outputStream = new FileOutputStream("C:/Temp/testFile2.mp4"); IOUtils.copy(inputStream, outputStream); inputStream.close(); outputStream.close(); } | 885,779 |
0 | public void insertStringInFile(String file, String textToInsert, long fromByte, long toByte) throws Exception { String tmpFile = file + ".tmp"; BufferedInputStream in = null; BufferedOutputStream out = null; long byteCount = 0; try { in = new BufferedInputStream(new FileInputStream(new File(file))); out = new BufferedOutputStream(new FileOutputStream(tmpFile)); long size = fromByte; byte[] buf = null; if (size == 0) { } else { buf = new byte[(int) size]; int length = -1; if ((length = in.read(buf)) != -1) { out.write(buf, 0, length); byteCount = byteCount + length; } else { String msg = "Failed to read the first '" + size + "' bytes of file '" + file + "'. This might be a programming error."; this.logger.warning(msg); throw new Exception(msg); } } buf = textToInsert.getBytes(); int length = buf.length; out.write(buf, 0, length); byteCount = byteCount + length; long skipLength = toByte - fromByte; long skippedBytes = in.skip(skipLength); if (skippedBytes == -1) { } else { buf = new byte[4096]; length = -1; while ((length = in.read(buf)) != -1) { out.write(buf, 0, length); byteCount = byteCount + length; } } in.close(); in = null; out.close(); out = null; File fileToDelete = new File(file); boolean wasDeleted = fileToDelete.delete(); if (!wasDeleted) { String msg = "Failed to delete the original file '" + file + "' to replace it with the modified file after text insertion."; this.logger.warning(msg); throw new Exception(msg); } File fileToRename = new File(tmpFile); boolean wasRenamed = fileToRename.renameTo(fileToDelete); if (!wasRenamed) { String msg = "Failed to rename tmp file '" + tmpFile + "' to the name of the original file '" + file + "'"; this.logger.warning(msg); throw new Exception(msg); } } catch (Exception e) { this.logger.log(Level.WARNING, "Failed to read/write file '" + file + "'.", e); throw e; } finally { if (in != null) { try { in.close(); } catch (IOException e) { this.logger.log(Level.FINEST, "Ignoring error closing input file '" + file + "'.", e); } } if (out != null) { try { out.close(); } catch (IOException e) { this.logger.log(Level.FINEST, "Ignoring error closing output file '" + tmpFile + "'.", e); } } } } | public String readCustomTemplate(String spaceKey) throws LocalizedException { final URL url = this.findTemplate(spaceKey); if (url == null) { return spaceKey == null ? this.readDefaultTemplate() : this.readCustomTemplate(null); } else try { return read(url.openStream()); } catch (IOException exception) { throw new LocalizedException(this, "reading.custom", spaceKey, exception); } } | 885,780 |
0 | public void testConnectionManagerGC() throws Exception { ThreadSafeClientConnManager mgr = createTSCCM(null, null); final HttpHost target = getServerHttp(); final HttpRoute route = new HttpRoute(target, null, false); final int rsplen = 8; final String uri = "/random/" + rsplen; HttpRequest request = new BasicHttpRequest("GET", uri, HttpVersion.HTTP_1_1); ManagedClientConnection conn = getConnection(mgr, route); conn.open(route, httpContext, defaultParams); HttpResponse response = Helper.execute(request, conn, target, httpExecutor, httpProcessor, defaultParams, httpContext); EntityUtils.toByteArray(response.getEntity()); conn.markReusable(); mgr.releaseConnection(conn, -1, null); WeakReference<ThreadSafeClientConnManager> wref = new WeakReference<ThreadSafeClientConnManager>(mgr); mgr = null; System.gc(); Thread.sleep(1000); assertNull("TSCCM not garbage collected", wref.get()); } | public static String encrypt(String passPhrase, String password) { String algorithm = "PBEWithMD5AndDES"; byte[] salt = new byte[8]; int iterations = 20; byte[] output = new byte[128]; if (passPhrase == null || "".equals(passPhrase) || password == null || "".equals(password)) { throw new GeneralException(PassPhraseCrypto.class, "encrypt", "Required parameter missing"); } try { Security.addProvider(new com.sun.crypto.provider.SunJCE()); KeySpec keySpec = new PBEKeySpec(passPhrase.toCharArray()); SecretKeyFactory secretKeyFactory = SecretKeyFactory.getInstance(algorithm); SecretKey secretKey = secretKeyFactory.generateSecret(keySpec); MessageDigest messageDigest = MessageDigest.getInstance("MD5"); messageDigest.update(passPhrase.getBytes()); byte[] input = new byte[password.length()]; input = password.getBytes(); messageDigest.update(input); byte[] digest = messageDigest.digest(); System.arraycopy(digest, 0, salt, 0, 8); AlgorithmParameterSpec algorithmParameterSpec = new PBEParameterSpec(salt, iterations); Cipher cipher = Cipher.getInstance(algorithm); int mode = Cipher.ENCRYPT_MODE; cipher.init(mode, secretKey, algorithmParameterSpec); output = cipher.doFinal(input); } catch (NoSuchAlgorithmException e) { throw new GeneralException(PassPhraseCrypto.class, "encrypt", "Algorithm not found", e); } catch (InvalidAlgorithmParameterException e) { throw new GeneralException(PassPhraseCrypto.class, "encrypt", "nvalidAlgorithmParameter", e); } catch (InvalidKeySpecException e) { throw new GeneralException(PassPhraseCrypto.class, "encrypt", "InvalidKeySpec", e); } catch (InvalidKeyException e) { throw new GeneralException(PassPhraseCrypto.class, "encrypt", "InvalidKey", e); } catch (NoSuchPaddingException e) { throw new GeneralException(PassPhraseCrypto.class, "encrypt", "NoSuchPadding", e); } catch (BadPaddingException e) { throw new GeneralException(PassPhraseCrypto.class, "encrypt", "BadPadding", e); } catch (IllegalBlockSizeException e) { throw new GeneralException(PassPhraseCrypto.class, "encrypt", "IllegalBlockSize", e); } StringBuffer result = new StringBuffer(); for (int i = 0; i < output.length; i++) { result.append(Byte.toString(output[i])); } return result.toString(); } | 885,781 |
0 | public static String MD5(String text) throws ProducteevSignatureException { try { MessageDigest md; md = MessageDigest.getInstance(ALGORITHM); byte[] md5hash; md.update(text.getBytes("utf-8"), 0, text.length()); md5hash = md.digest(); return convertToHex(md5hash); } catch (NoSuchAlgorithmException nsae) { throw new ProducteevSignatureException("No such algorithm : " + ALGORITHM, nsae); } catch (UnsupportedEncodingException e) { throw new ProducteevSignatureException("No such algorithm : " + ALGORITHM, e); } } | @Override protected final void doGet(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException { if (beforeServingFile(req, resp)) { String pathInfo = req.getPathInfo(); Validate.notNull(pathInfo, "the path info is null -> the sevlet should be mapped with /<mapping>/*"); String resurouce = pathInfo.substring(1); if (log.isDebugEnabled()) { log.debug("resource to expose: " + resurouce); } String extension = resurouce.substring(resurouce.lastIndexOf('.') + 1); MimeType mimeType = MimeTypeRegistry.getByExtension(extension); Validate.notNull(mimeType, "no mimetype found for extension: " + extension); if (log.isDebugEnabled()) { log.debug("the mime type to set: " + mimeType.getMimeType()); } File f = new File(mappedFolder, resurouce); Validate.isTrue(f.exists(), "file: " + f + " does not exist"); Validate.isTrue(f.canRead(), "can not read the file: " + f); if (log.isDebugEnabled()) { log.debug("exposing the file: " + f); } resp.setContentType(mimeType.getMimeType()); FileInputStream fis = new FileInputStream(f); ServletOutputStream os = resp.getOutputStream(); IOUtils.copy(fis, os); os.flush(); IOUtils.closeQuietly(fis); IOUtils.closeQuietly(os); } } | 885,782 |
1 | public static String generateMessageId(String plain) { byte[] cipher = new byte[35]; String messageId = null; try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(plain.getBytes()); cipher = md5.digest(); StringBuffer sb = new StringBuffer(); for (int i = 0; i < cipher.length; i++) { String hex = Integer.toHexString(0xff & cipher[i]); if (hex.length() == 1) sb.append('0'); sb.append(hex); } StringBuffer pass = new StringBuffer(); pass.append(sb.substring(0, 6)); pass.append("H"); pass.append(sb.substring(6, 11)); pass.append("H"); pass.append(sb.substring(11, 21)); pass.append("H"); pass.append(sb.substring(21)); messageId = new String(pass); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } return messageId; } | private static String deviceIdFromCombined_Device_ID(Context context) { StringBuilder builder = new StringBuilder(); builder.append(deviceIdFromIMEI(context)); builder.append(deviceIdFromPseudo_Unique_Id()); builder.append(deviceIdFromAndroidId(context)); builder.append(deviceIdFromWLAN_MAC_Address(context)); builder.append(deviceIdFromBT_MAC_Address(context)); String m_szLongID = builder.toString(); MessageDigest m = null; try { m = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } m.update(m_szLongID.getBytes(), 0, m_szLongID.length()); byte p_md5Data[] = m.digest(); String m_szUniqueID = new String(); for (int i = 0; i < p_md5Data.length; i++) { int b = (0xFF & p_md5Data[i]); if (b <= 0xF) m_szUniqueID += "0"; m_szUniqueID += Integer.toHexString(b); } return m_szUniqueID; } | 885,783 |
1 | public static void copy(File source, File dest) throws Exception { FileInputStream in = new FileInputStream(source); FileOutputStream out = new FileOutputStream(dest); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } | public void send(org.hibernate.Session hsession, Session session, String repositoryName, Vector files, int label, String charset) throws FilesException { ByteArrayInputStream bais = null; FileOutputStream fos = null; try { if ((files == null) || (files.size() <= 0)) { return; } if (charset == null) { charset = MimeUtility.javaCharset(Charset.defaultCharset().displayName()); } Users user = getUser(hsession, repositoryName); Identity identity = getDefaultIdentity(hsession, user); InternetAddress _returnPath = new InternetAddress(identity.getIdeEmail(), identity.getIdeName()); InternetAddress _from = new InternetAddress(identity.getIdeEmail(), identity.getIdeName()); InternetAddress _replyTo = new InternetAddress(identity.getIdeReplyTo(), identity.getIdeName()); InternetAddress _to = new InternetAddress(identity.getIdeEmail(), identity.getIdeName()); for (int i = 0; i < files.size(); i++) { MultiPartEmail email = email = new MultiPartEmail(); email.setCharset(charset); if (_from != null) { email.setFrom(_from.getAddress(), _from.getPersonal()); } if (_returnPath != null) { email.addHeader("Return-Path", _returnPath.getAddress()); email.addHeader("Errors-To", _returnPath.getAddress()); email.addHeader("X-Errors-To", _returnPath.getAddress()); } if (_replyTo != null) { email.addReplyTo(_replyTo.getAddress(), _replyTo.getPersonal()); } if (_to != null) { email.addTo(_to.getAddress(), _to.getPersonal()); } MailPartObj obj = (MailPartObj) files.get(i); email.setSubject("Files-System " + obj.getName()); Date now = new Date(); email.setSentDate(now); File dir = new File(System.getProperty("user.home") + File.separator + "tmp"); if (!dir.exists()) { dir.mkdir(); } File file = new File(dir, obj.getName()); bais = new ByteArrayInputStream(obj.getAttachent()); fos = new FileOutputStream(file); IOUtils.copy(bais, fos); IOUtils.closeQuietly(bais); IOUtils.closeQuietly(fos); EmailAttachment attachment = new EmailAttachment(); attachment.setPath(file.getPath()); attachment.setDisposition(EmailAttachment.ATTACHMENT); attachment.setDescription("File Attachment: " + file.getName()); attachment.setName(file.getName()); email.attach(attachment); String mid = getId(); email.addHeader(RFC2822Headers.IN_REPLY_TO, "<" + mid + ".JavaMail.duroty@duroty" + ">"); email.addHeader(RFC2822Headers.REFERENCES, "<" + mid + ".JavaMail.duroty@duroty" + ">"); email.addHeader("X-DBox", "FILES"); email.addHeader("X-DRecent", "false"); email.setMailSession(session); email.buildMimeMessage(); MimeMessage mime = email.getMimeMessage(); int size = MessageUtilities.getMessageSize(mime); if (!controlQuota(hsession, user, size)) { throw new MailException("ErrorMessages.mail.quota.exceded"); } messageable.storeMessage(mid, mime, user); } } catch (FilesException e) { throw e; } catch (Exception e) { throw new FilesException(e); } catch (java.lang.OutOfMemoryError ex) { System.gc(); throw new FilesException(ex); } catch (Throwable e) { throw new FilesException(e); } finally { GeneralOperations.closeHibernateSession(hsession); IOUtils.closeQuietly(bais); IOUtils.closeQuietly(fos); } } | 885,784 |
0 | public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | public static void refreshSession(int C_ID) { Connection con = null; try { con = getConnection(); PreparedStatement updateLogin = con.prepareStatement("UPDATE customer SET c_login = NOW(), c_expiration = DATE_ADD(NOW(), INTERVAL 2 HOUR) WHERE c_id = ?"); updateLogin.setInt(1, C_ID); updateLogin.executeUpdate(); con.commit(); updateLogin.close(); returnConnection(con); } catch (java.lang.Exception ex) { try { con.rollback(); ex.printStackTrace(); } catch (Exception se) { System.err.println("Transaction rollback failed."); } } } | 885,785 |
0 | public String getNextObjectId() throws SQLException { long nextserial = 1; String s0 = "lock table serials in exclusive mode"; String s1 = "SELECT nextserial FROM serials WHERE tablename = 'SERVER_OIDS'"; String s2; try { Statement stmt = dbconnect.connection.createStatement(); stmt.executeUpdate(s0); ResultSet rs = stmt.executeQuery(s1); if (!rs.next()) { s2 = "insert into serials (tablename,nextserial) values ('SERVER_OIDS', " + (nextserial) + ")"; } else { nextserial = rs.getLong(1) + 1; s2 = "update serials set nextserial=" + (nextserial) + " where tablename='SERVER_OIDS'"; } stmt.executeUpdate(s2); dbconnect.connection.commit(); rs.close(); stmt.close(); return "" + nextserial; } catch (SQLException e) { dbconnect.connection.rollback(); throw e; } } | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | 885,786 |
0 | @Override public RoleItem addUserRole(RoleItem role, long userId) throws DatabaseException { if (role == null) throw new NullPointerException("role"); if (role.getName() == null || "".equals(role.getName())) throw new NullPointerException("role.getName()"); if (hasRole(role.getName(), userId)) { return new RoleItem(role.getName(), "", "exist"); } RoleItem defaultRole = new RoleItem(role.getName(), "", "exist"); try { getConnection().setAutoCommit(false); } catch (SQLException e) { LOGGER.warn("Unable to set autocommit off", e); } String retID = "exist"; String roleDesc = ""; PreparedStatement seqSt = null, roleDescSt = null; try { int modified = 0; PreparedStatement insSt = getConnection().prepareStatement(INSERT_USER_IN_ROLE_STATEMENT); insSt.setLong(1, userId); insSt.setString(2, role.getName()); modified = insSt.executeUpdate(); seqSt = getConnection().prepareStatement(USER_ROLE_VALUE); ResultSet rs = seqSt.executeQuery(); while (rs.next()) { retID = rs.getString(1); } roleDescSt = getConnection().prepareStatement(SELECT_ROLE_DESCRIPTION); roleDescSt.setString(1, role.getName()); ResultSet rs2 = roleDescSt.executeQuery(); while (rs2.next()) { roleDesc = rs2.getString(1); } if (modified == 1) { getConnection().commit(); LOGGER.debug("DB has been updated. Queries: \"" + seqSt + "\" and \"" + roleDescSt + "\""); } else { getConnection().rollback(); LOGGER.error("DB has not been updated -> rollback! Queries: \"" + seqSt + "\" and \"" + roleDescSt + "\""); retID = "error"; } } catch (SQLException e) { LOGGER.error(e); retID = "error"; } finally { closeConnection(); } defaultRole.setId(retID); defaultRole.setDescription(roleDesc); return defaultRole; } | public static void main(String[] args) { try { File fichierXSD = new File("D:/Users/Balley/données/gml/commune.xsd"); URL urlFichierXSD = fichierXSD.toURI().toURL(); InputStream isXSD = urlFichierXSD.openStream(); DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance(); DocumentBuilder builder = dbFactory.newDocumentBuilder(); Document documentXSD = (builder.parse(isXSD)); ChargeurGMLSchema chargeur = new ChargeurGMLSchema(documentXSD); SchemaConceptuelJeu sc = chargeur.gmlSchema2schemaConceptuel(documentXSD); System.out.println(sc.getFeatureTypes().size()); for (int i = 0; i < sc.getFeatureTypes().size(); i++) { System.out.println(sc.getFeatureTypes().get(i).getTypeName()); for (int j = 0; j < sc.getFeatureTypes().get(i).getFeatureAttributes().size(); j++) { System.out.println(" " + sc.getFeatureTypes().get(i).getFeatureAttributes().get(j).getMemberName() + " : " + sc.getFeatureTypes().get(i).getFeatureAttributes().get(j).getValueType()); } } } catch (MalformedURLException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } catch (ParserConfigurationException e) { e.printStackTrace(); } catch (SAXException e) { e.printStackTrace(); } } | 885,787 |
0 | private static void testIfModified() throws IOException { HttpURLConnection c2 = (HttpURLConnection) url.openConnection(); c2.setIfModifiedSince(System.currentTimeMillis() + 1000); c2.connect(); int code = c2.getResponseCode(); System.out.print("If-Modified-Since : "); boolean supported = (code == 304); System.out.println(b2s(supported) + " - " + code + " (" + c2.getResponseMessage() + ")"); } | public static void copyFile(File source, File destination) { if (!source.exists()) { return; } if ((destination.getParentFile() != null) && (!destination.getParentFile().exists())) { destination.getParentFile().mkdirs(); } try { FileChannel srcChannel = new FileInputStream(source).getChannel(); FileChannel dstChannel = new FileOutputStream(destination).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException ioe) { ioe.printStackTrace(); } } | 885,788 |
1 | public String encrypt(String plaintext) throws Exception { MessageDigest md = null; try { md = MessageDigest.getInstance("SHA"); } catch (NoSuchAlgorithmException e) { throw new Exception(e.getMessage()); } try { md.update(plaintext.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { throw new Exception(e.getMessage()); } byte raw[] = md.digest(); String hash = (new BASE64Encoder()).encode(raw); return hash; } | @SmallTest public void testSha1() throws Exception { MessageDigest digest = MessageDigest.getInstance("SHA-1"); int numTests = mTestData.length; for (int i = 0; i < numTests; i++) { digest.update(mTestData[i].input.getBytes()); byte[] hash = digest.digest(); String encodedHash = encodeHex(hash); assertEquals(encodedHash, mTestData[i].result); } } | 885,789 |
0 | public LOCKSSDaemonStatusTableTO getDataFromDaemonStatusTableByHttps() throws HttpResponseException { LOCKSSDaemonStatusTableXmlStreamParser ldstxp = null; LOCKSSDaemonStatusTableTO ldstTO = null; HttpEntity entity = null; HttpGet httpget = null; xstream.setMode(XStream.NO_REFERENCES); xstream.alias("HttpClientDAO", HttpClientDAO.class); try { httpget = new HttpGet(dataUrl); logger.log(Level.INFO, "executing request {0}", httpget.getURI()); HttpResponse resp = httpClient.execute(httpget); int statusCode = resp.getStatusLine().getStatusCode(); if (statusCode != HttpStatus.SC_OK) { logger.log(Level.WARNING, "response to the request is not OK: skip this IP: status code={0}", statusCode); httpget.abort(); ldstTO = new LOCKSSDaemonStatusTableTO(); ldstTO.setBoxHttpStatusOK(false); return ldstTO; } entity = resp.getEntity(); InputStream is = entity.getContent(); ldstxp = new LOCKSSDaemonStatusTableXmlStreamParser(); ldstxp.read(new BufferedInputStream(is)); ldstTO = ldstxp.getLOCKSSDaemonStatusTableTO(); ldstTO.setIpAddress(this.ip); logger.log(Level.INFO, "After parsing [{0}] table", this.tableId); logger.log(Level.FINEST, "After parsing {0}: contents of ldstTO:\n{1}", new Object[] { this.tableId, ldstTO }); if (ldstTO.hasIncompleteRows) { logger.log(Level.WARNING, "!!!!!!!!! incomplete rows are found for {0}", tableId); if (ldstTO.getTableData() != null && ldstTO.getTableData().size() > 0) { logger.log(Level.FINE, "incomplete rows: table(map) data dump =[\n{0}\n]", xstream.toXML(ldstTO.getTableData())); } } else { logger.log(Level.INFO, "All rows are complete for {0}", tableId); } } catch (ConnectTimeoutException ce) { logger.log(Level.WARNING, "ConnectTimeoutException occurred", ce); ldstTO = new LOCKSSDaemonStatusTableTO(); ldstTO.setBoxHttpStatusOK(false); if (httpget != null) { httpget.abort(); } return ldstTO; } catch (SocketTimeoutException se) { logger.log(Level.WARNING, "SocketTimeoutException occurred", se); ldstTO = new LOCKSSDaemonStatusTableTO(); ldstTO.setBoxHttpStatusOK(false); if (httpget != null) { httpget.abort(); } return ldstTO; } catch (ClientProtocolException pe) { logger.log(Level.SEVERE, "The protocol was not http; https is suspected", pe); ldstTO = new LOCKSSDaemonStatusTableTO(); ldstTO.setBoxHttpStatusOK(false); ldstTO.setHttpProtocol(false); if (httpget != null) { httpget.abort(); } return ldstTO; } catch (IOException ex) { logger.log(Level.SEVERE, "IO exception occurs", ex); ldstTO = new LOCKSSDaemonStatusTableTO(); ldstTO.setBoxHttpStatusOK(false); if (httpget != null) { httpget.abort(); } return ldstTO; } finally { if (entity != null) { try { EntityUtils.consume(entity); } catch (IOException ex) { logger.log(Level.SEVERE, "io exception when entity was to be" + "consumed", ex); } } } return ldstTO; } | public static void pingSearchEngine(String engineURL) throws MalformedURLException, UnsupportedEncodingException { if ((ConfigurationManager.getProperty("http.proxy.host") != null) && (ConfigurationManager.getProperty("http.proxy.port") != null)) { System.setProperty("proxySet", "true"); System.setProperty("proxyHost", ConfigurationManager.getProperty("http.proxy.host")); System.getProperty("proxyPort", ConfigurationManager.getProperty("http.proxy.port")); } String sitemapURL = ConfigurationManager.getProperty("dspace.url") + "/sitemap"; URL url = new URL(engineURL + URLEncoder.encode(sitemapURL, "UTF-8")); try { HttpURLConnection connection = (HttpURLConnection) url.openConnection(); BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream())); String inputLine; StringBuffer resp = new StringBuffer(); while ((inputLine = in.readLine()) != null) { resp.append(inputLine).append("\n"); } in.close(); if (connection.getResponseCode() == 200) { log.info("Pinged " + url.toString() + " successfully"); } else { log.warn("Error response pinging " + url.toString() + ":\n" + resp); } } catch (IOException e) { log.warn("Error pinging " + url.toString(), e); } } | 885,790 |
1 | public static void copy(File source, File sink) throws IOException { if (source == null) throw new NullPointerException("Source file must not be null"); if (sink == null) throw new NullPointerException("Target file must not be null"); if (!source.exists()) throw new IOException("Source file " + source.getPath() + " does not exist"); if (!source.isFile()) throw new IOException("Source file " + source.getPath() + " is not a regular file"); if (!source.canRead()) throw new IOException("Source file " + source.getPath() + " can not be read (missing acces right)"); if (!sink.exists()) throw new IOException("Target file " + sink.getPath() + " does not exist"); if (!sink.isFile()) throw new IOException("Target file " + sink.getPath() + " is not a regular file"); if (!sink.canWrite()) throw new IOException("Target file " + sink.getPath() + " is write protected"); InputStream input = null; OutputStream output = null; try { input = new FileInputStream(source); output = new FileOutputStream(sink); byte[] buffer = new byte[1024]; while (input.available() > 0) { int bread = input.read(buffer); if (bread > 0) output.write(buffer, 0, bread); } } finally { if (input != null) try { input.close(); } catch (IOException x) { } if (output != null) try { output.close(); } catch (IOException x) { } } } | public static void copyFile(File inputFile, File outputFile) throws IOException { BufferedInputStream fr = new BufferedInputStream(new FileInputStream(inputFile)); BufferedOutputStream fw = new BufferedOutputStream(new FileOutputStream(outputFile)); byte[] buf = new byte[8192]; int n; while ((n = fr.read(buf)) >= 0) fw.write(buf, 0, n); fr.close(); fw.close(); } | 885,791 |
1 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | public static void copyFile(File in, File out) throws IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); FileChannel outChannel = new FileOutputStream(out).getChannel(); try { int maxCount = (64 * 1024 * 1024) - (32 * 1024); long size = inChannel.size(); long position = 0; while (position < size) { position += inChannel.transferTo(position, maxCount, outChannel); } out.setLastModified(in.lastModified()); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } } | 885,792 |
0 | @Override protected void doGet(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException { String contentId = req.getParameter(CONTENT_ID); String contentType = req.getParameter(CONTENT_TYPE); if (contentId == null || contentType == null) { resp.sendError(HttpServletResponse.SC_BAD_REQUEST, "Content id or content type not specified"); return; } try { switch(ContentType.valueOf(contentType)) { case IMAGE: resp.setContentType("image/jpeg"); break; case AUDIO: resp.setContentType("audio/mp3"); break; case VIDEO: resp.setContentType("video/mpeg"); break; default: throw new IllegalStateException("Invalid content type specified"); } } catch (IllegalArgumentException e) { resp.sendError(HttpServletResponse.SC_BAD_REQUEST, "Invalid content type specified"); return; } String baseUrl = this.getServletContext().getInitParameter(BASE_URL); URL url = new URL(baseUrl + "/" + contentType.toLowerCase() + "/" + contentId); URLConnection conn = url.openConnection(); resp.setContentLength(conn.getContentLength()); IOUtils.copy(conn.getInputStream(), resp.getOutputStream()); } | public APIResponse delete(String id) throws Exception { APIResponse response = new APIResponse(); connection = (HttpURLConnection) new URL(url + "/api/transaction/delete/" + id).openConnection(); connection.setRequestMethod("DELETE"); connection.setConnectTimeout(TIMEOUT); connection.connect(); if (connection.getResponseCode() == HttpURLConnection.HTTP_OK) { response.setDone(true); response.setMessage("Transaction Deleted!"); } else { response.setDone(false); response.setMessage("Delete Transaction Error Code: Http (" + connection.getResponseCode() + ")"); } connection.disconnect(); return response; } | 885,793 |
0 | private final Vector<Class<?>> findSubclasses(URL location, String packageName, Class<?> superClass) { synchronized (results) { Map<Class<?>, URL> thisResult = new TreeMap<Class<?>, URL>(CLASS_COMPARATOR); Vector<Class<?>> v = new Vector<Class<?>>(); String fqcn = searchClass.getName(); List<URL> knownLocations = new ArrayList<URL>(); knownLocations.add(location); for (int loc = 0; loc < knownLocations.size(); loc++) { URL url = knownLocations.get(loc); File directory = new File(url.getFile()); if (directory.exists()) { String[] files = directory.list(); for (int i = 0; i < files.length; i++) { if (files[i].endsWith(".class")) { String classname = files[i].substring(0, files[i].length() - 6); try { Class<?> c = Class.forName(packageName + "." + classname); if (superClass.isAssignableFrom(c) && !fqcn.equals(packageName + "." + classname)) { thisResult.put(c, url); } } catch (ClassNotFoundException cnfex) { if (debug) { errors.add(cnfex); } } catch (Exception ex) { if (debug) { errors.add(ex); } } catch (NoClassDefFoundError ncdfe) { if (debug) { errors.add(ncdfe); } } } } } else { try { JarURLConnection conn = (JarURLConnection) url.openConnection(); JarFile jarFile = conn.getJarFile(); Enumeration<JarEntry> e = jarFile.entries(); while (e.hasMoreElements()) { JarEntry entry = e.nextElement(); String entryname = entry.getName(); if (!entry.isDirectory() && entryname.endsWith(".class")) { String classname = entryname.substring(0, entryname.length() - 6); if (classname.startsWith("/")) classname = classname.substring(1); classname = classname.replace('/', '.'); try { Class c = Class.forName(classname); if (superClass.isAssignableFrom(c) && !fqcn.equals(classname)) { thisResult.put(c, url); } } catch (ClassNotFoundException cnfex) { errors.add(cnfex); } catch (NoClassDefFoundError ncdfe) { errors.add(ncdfe); } catch (UnsatisfiedLinkError ule) { errors.add(ule); } catch (Exception exception) { errors.add(exception); } catch (Error error) { errors.add(error); } } } } catch (IOException ioex) { errors.add(ioex); } } } results.putAll(thisResult); Iterator<Class<?>> it = thisResult.keySet().iterator(); while (it.hasNext()) { v.add(it.next()); } return v; } } | public String preProcessHTML(String uri) { final StringBuffer buf = new StringBuffer(); try { HTMLDocument doc = new HTMLDocument() { public HTMLEditorKit.ParserCallback getReader(int pos) { return new HTMLEditorKit.ParserCallback() { public void handleText(char[] data, int pos) { buf.append(data); buf.append('\n'); } }; } }; URL url = new URI(uri).toURL(); URLConnection conn = url.openConnection(); Reader rd = new InputStreamReader(conn.getInputStream()); new ParserDelegator().parse(rd, doc.getReader(0), Boolean.TRUE); } catch (MalformedURLException e) { System.err.println(e.getMessage()); e.printStackTrace(); } catch (URISyntaxException e) { System.err.println(e.getMessage()); e.printStackTrace(); } catch (IOException e) { System.err.println(e.getMessage()); e.printStackTrace(); } return buf.toString(); } | 885,794 |
1 | public static final void copy(File src, File dest) throws IOException { FileInputStream source = null; FileOutputStream destination = null; byte[] buffer; int bytes_read; if (!src.exists()) { throw new IOException("Source not found: " + src); } if (!src.canRead()) { throw new IOException("Source is unreadable: " + src); } if (src.isFile()) { if (!dest.exists()) { File parentdir = parent(dest); if (!parentdir.exists()) { parentdir.mkdir(); } } else if (dest.isDirectory()) { dest = new File(dest + File.separator + src); } } else if (src.isDirectory()) { if (dest.isFile()) { throw new IOException("Cannot copy directory " + src + " to file " + dest); } if (!dest.exists()) { dest.mkdir(); } } if (src.isFile()) { try { source = new FileInputStream(src); destination = new FileOutputStream(dest); buffer = new byte[1024]; while (true) { bytes_read = source.read(buffer); if (bytes_read == -1) { break; } destination.write(buffer, 0, bytes_read); } } finally { if (source != null) { try { source.close(); } catch (IOException e) { } } if (destination != null) { try { destination.close(); } catch (IOException e) { } } } } else if (src.isDirectory()) { String targetfile, target, targetdest; String[] files = src.list(); for (int i = 0; i < files.length; i++) { targetfile = files[i]; target = src + File.separator + targetfile; targetdest = dest + File.separator + targetfile; if ((new File(target)).isDirectory()) { copy(new File(target), new File(targetdest)); } else { try { source = new FileInputStream(target); destination = new FileOutputStream(targetdest); buffer = new byte[1024]; while (true) { bytes_read = source.read(buffer); if (bytes_read == -1) { break; } destination.write(buffer, 0, bytes_read); } } finally { if (source != null) { try { source.close(); } catch (IOException e) { } } if (destination != null) { try { destination.close(); } catch (IOException e) { } } } } } } } | public static boolean decodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.DECODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | 885,795 |
0 | public void extractProfile(String parentDir, String fileName, String profileName) { try { byte[] buf = new byte[1024]; ZipInputStream zipinputstream = null; ZipEntry zipentry; if (createProfileDirectory(profileName, parentDir)) { debug("the profile directory created .starting the profile extraction"); String profilePath = parentDir + File.separator + fileName; zipinputstream = new ZipInputStream(new FileInputStream(profilePath)); zipentry = zipinputstream.getNextEntry(); while (zipentry != null) { String entryName = zipentry.getName(); int n; FileOutputStream fileoutputstream; File newFile = new File(entryName); String directory = newFile.getParent(); if (directory == null) { if (newFile.isDirectory()) break; } fileoutputstream = new FileOutputStream(parentDir + File.separator + profileName + File.separator + newFile.getName()); while ((n = zipinputstream.read(buf, 0, 1024)) > -1) fileoutputstream.write(buf, 0, n); fileoutputstream.close(); zipinputstream.closeEntry(); zipentry = zipinputstream.getNextEntry(); } zipinputstream.close(); debug("deleting the profile.zip file"); File newFile = new File(profilePath); if (newFile.delete()) { debug("the " + "[" + profilePath + "]" + " deleted successfully"); } else { debug("profile" + "[" + profilePath + "]" + "deletion fail"); throw new IllegalArgumentException("Error: deletion error!"); } } else { debug("error creating the profile directory"); } } catch (Exception e) { e.printStackTrace(); } } | private static String doHash(String frase, String algorithm) { try { String ret; MessageDigest md = MessageDigest.getInstance(algorithm); md.update(frase.getBytes()); BigInteger bigInt = new BigInteger(1, md.digest()); ret = bigInt.toString(16); return ret; } catch (NoSuchAlgorithmException e) { return null; } } | 885,796 |
0 | @Override public void start() { System.err.println("start AutoplotApplet " + VERSION + " @ " + (System.currentTimeMillis() - t0) + " msec"); super.start(); model = new ApplicationModel(); model.setExceptionHandler(new ExceptionHandler() { public void handle(Throwable t) { t.printStackTrace(); } public void handleUncaught(Throwable t) { t.printStackTrace(); } }); model.setApplet(true); model.dom.getOptions().setAutolayout(false); System.err.println("ApplicationModel created @ " + (System.currentTimeMillis() - t0) + " msec"); model.addDasPeersToApp(); System.err.println("done addDasPeersToApp @ " + (System.currentTimeMillis() - t0) + " msec"); try { System.err.println("Formatters: " + DataSourceRegistry.getInstance().getFormatterExtensions()); } catch (Exception ex) { Logger.getLogger(AutoplotApplet.class.getName()).log(Level.SEVERE, null, ex); } ApplicationModel appmodel = model; dom = model.getDocumentModel(); String debug = getParameter("debug"); if (debug != null && !debug.equals("true")) { } int width = getIntParameter("width", 700); int height = getIntParameter("height", 400); String fontParam = getStringParameter("font", ""); String column = getStringParameter("column", ""); String row = getStringParameter("row", ""); String scolor = getStringParameter("color", ""); String srenderType = getStringParameter("renderType", ""); String stimeRange = getStringParameter("timeRange", ""); String sfillColor = getStringParameter("fillColor", ""); String sforegroundColor = getStringParameter("foregroundColor", ""); String sbackgroundColor = getStringParameter("backgroundColor", ""); String title = getStringParameter("plot.title", ""); String xlabel = getStringParameter("plot.xaxis.label", ""); String xrange = getStringParameter("plot.xaxis.range", ""); String xlog = getStringParameter("plot.xaxis.log", ""); String xdrawTickLabels = getStringParameter("plot.xaxis.drawTickLabels", ""); String ylabel = getStringParameter("plot.yaxis.label", ""); String yrange = getStringParameter("plot.yaxis.range", ""); String ylog = getStringParameter("plot.yaxis.log", ""); String ydrawTickLabels = getStringParameter("plot.yaxis.drawTickLabels", ""); String zlabel = getStringParameter("plot.zaxis.label", ""); String zrange = getStringParameter("plot.zaxis.range", ""); String zlog = getStringParameter("plot.zaxis.log", ""); String zdrawTickLabels = getStringParameter("plot.zaxis.drawTickLabels", ""); statusCallback = getStringParameter("statusCallback", ""); timeCallback = getStringParameter("timeCallback", ""); clickCallback = getStringParameter("clickCallback", ""); if (srenderType.equals("fill_to_zero")) { srenderType = "fillToZero"; } setInitializationStatus("readParameters"); System.err.println("done readParameters @ " + (System.currentTimeMillis() - t0) + " msec"); String vap = getParameter("vap"); if (vap != null) { InputStream in = null; try { URL url = new URL(vap); System.err.println("load vap " + url + " @ " + (System.currentTimeMillis() - t0) + " msec"); in = url.openStream(); System.err.println("open vap stream " + url + " @ " + (System.currentTimeMillis() - t0) + " msec"); appmodel.doOpen(in, null); System.err.println("done open vap @ " + (System.currentTimeMillis() - t0) + " msec"); appmodel.waitUntilIdle(false); System.err.println("done load vap and waitUntilIdle @ " + (System.currentTimeMillis() - t0) + " msec"); Canvas cc = appmodel.getDocumentModel().getCanvases(0); System.err.println("vap height, width= " + cc.getHeight() + "," + cc.getWidth()); width = getIntParameter("width", cc.getWidth()); height = getIntParameter("height", cc.getHeight()); System.err.println("output height, width= " + width + "," + height); } catch (InterruptedException ex) { Logger.getLogger(AutoplotApplet.class.getName()).log(Level.SEVERE, null, ex); } catch (IOException ex) { Logger.getLogger(AutoplotApplet.class.getName()).log(Level.SEVERE, null, ex); } finally { try { in.close(); } catch (IOException ex) { Logger.getLogger(AutoplotApplet.class.getName()).log(Level.SEVERE, null, ex); } } } appmodel.getCanvas().setSize(width, height); appmodel.getCanvas().revalidate(); appmodel.getCanvas().setPrintingTag(""); dom.getOptions().setAutolayout("true".equals(getParameter("autolayout"))); if (!dom.getOptions().isAutolayout() && vap == null) { if (!row.equals("")) { dom.getController().getCanvas().getController().setRow(row); } if (!column.equals("")) { dom.getController().getCanvas().getController().setColumn(column); } dom.getCanvases(0).getRows(0).setTop("0%"); dom.getCanvases(0).getRows(0).setBottom("100%"); } if (!fontParam.equals("")) { appmodel.canvas.setBaseFont(Font.decode(fontParam)); } JMenuItem item; item = new JMenuItem(new AbstractAction("Reset Zoom") { public void actionPerformed(ActionEvent e) { resetZoom(); } }); dom.getPlots(0).getController().getDasPlot().getDasMouseInputAdapter().addMenuItem(item); overviewMenuItem = new JCheckBoxMenuItem(new AbstractAction("Context Overview") { public void actionPerformed(ActionEvent e) { addOverview(); } }); dom.getPlots(0).getController().getDasPlot().getDasMouseInputAdapter().addMenuItem(overviewMenuItem); if (sforegroundColor != null && !sforegroundColor.equals("")) { appmodel.canvas.setForeground(Color.decode(sforegroundColor)); } if (sbackgroundColor != null && !sbackgroundColor.equals("")) { appmodel.canvas.setBackground(Color.decode(sbackgroundColor)); } getContentPane().setLayout(new BorderLayout()); System.err.println("done set parameters @ " + (System.currentTimeMillis() - t0) + " msec"); String surl = getParameter("url"); String process = getStringParameter("process", ""); String script = getStringParameter("script", ""); if (surl == null) { surl = getParameter("dataSetURL"); } if (surl != null && !surl.equals("")) { DataSource dsource; try { dsource = DataSetURI.getDataSource(surl); System.err.println("get dsource for " + surl + " @ " + (System.currentTimeMillis() - t0) + " msec"); System.err.println(" got dsource=" + dsource); System.err.println(" dsource.getClass()=" + dsource.getClass()); } catch (NullPointerException ex) { throw new RuntimeException("No such data source: ", ex); } catch (Exception ex) { ex.printStackTrace(); dsource = null; } DatumRange timeRange1 = null; if (!stimeRange.equals("")) { timeRange1 = DatumRangeUtil.parseTimeRangeValid(stimeRange); TimeSeriesBrowse tsb = dsource.getCapability(TimeSeriesBrowse.class); if (tsb != null) { System.err.println("do tsb.setTimeRange @ " + (System.currentTimeMillis() - t0) + " msec"); tsb.setTimeRange(timeRange1); System.err.println("done tsb.setTimeRange @ " + (System.currentTimeMillis() - t0) + " msec"); } } QDataSet ds; if (dsource != null) { TimeSeriesBrowse tsb = dsource.getCapability(TimeSeriesBrowse.class); if (tsb == null) { try { System.err.println("do getDataSet @ " + (System.currentTimeMillis() - t0) + " msec"); System.err.println(" dsource=" + dsource); System.err.println(" dsource.getClass()=" + dsource.getClass()); if (dsource.getClass().toString().contains("CsvDataSource")) System.err.println(" WHY IS THIS CsvDataSource!?!?"); ds = dsource == null ? null : dsource.getDataSet(loadInitialMonitor); for (int i = 0; i < Math.min(12, ds.length()); i++) { System.err.printf("ds[%d]=%s\n", i, ds.slice(i)); } System.err.println("loaded ds: " + ds); System.err.println("done getDataSet @ " + (System.currentTimeMillis() - t0) + " msec"); } catch (Exception ex) { throw new RuntimeException(ex); } } } System.err.println("do setDataSource @ " + (System.currentTimeMillis() - t0) + " msec"); appmodel.setDataSource(dsource); System.err.println("done setDataSource @ " + (System.currentTimeMillis() - t0) + " msec"); setInitializationStatus("dataSourceSet"); if (stimeRange != null && !stimeRange.equals("")) { try { System.err.println("wait for idle @ " + (System.currentTimeMillis() - t0) + " msec (due to stimeRange)"); appmodel.waitUntilIdle(true); System.err.println("done wait for idle @ " + (System.currentTimeMillis() - t0) + " msec"); } catch (InterruptedException ex) { Logger.getLogger(AutoplotApplet.class.getName()).log(Level.SEVERE, null, ex); } if (UnitsUtil.isTimeLocation(dom.getTimeRange().getUnits())) { dom.setTimeRange(timeRange1); } } setInitializationStatus("dataSetLoaded"); } System.err.println("done dataSetLoaded @ " + (System.currentTimeMillis() - t0) + " msec"); Plot p = dom.getController().getPlot(); if (!title.equals("")) { p.setTitle(title); } Axis axis = p.getXaxis(); if (!xlabel.equals("")) { axis.setLabel(xlabel); } if (!xrange.equals("")) { try { Units u = axis.getController().getDasAxis().getUnits(); DatumRange newRange = DatumRangeUtil.parseDatumRange(xrange, u); axis.setRange(newRange); } catch (ParseException ex) { Logger.getLogger(AutoplotApplet.class.getName()).log(Level.SEVERE, null, ex); } } if (!xlog.equals("")) { axis.setLog("true".equals(xlog)); } if (!xdrawTickLabels.equals("")) { axis.setDrawTickLabels("true".equals(xdrawTickLabels)); } axis = p.getYaxis(); if (!ylabel.equals("")) { axis.setLabel(ylabel); } if (!yrange.equals("")) { try { Units u = axis.getController().getDasAxis().getUnits(); DatumRange newRange = DatumRangeUtil.parseDatumRange(yrange, u); axis.setRange(newRange); } catch (ParseException ex) { Logger.getLogger(AutoplotApplet.class.getName()).log(Level.SEVERE, null, ex); } } if (!ylog.equals("")) { axis.setLog("true".equals(ylog)); } if (!ydrawTickLabels.equals("")) { axis.setDrawTickLabels("true".equals(ydrawTickLabels)); } axis = p.getZaxis(); if (!zlabel.equals("")) { axis.setLabel(zlabel); } if (!zrange.equals("")) { try { Units u = axis.getController().getDasAxis().getUnits(); DatumRange newRange = DatumRangeUtil.parseDatumRange(zrange, u); axis.setRange(newRange); } catch (ParseException ex) { Logger.getLogger(AutoplotApplet.class.getName()).log(Level.SEVERE, null, ex); } } if (!zlog.equals("")) { axis.setLog("true".equals(zlog)); } if (!zdrawTickLabels.equals("")) { axis.setDrawTickLabels("true".equals(zdrawTickLabels)); } if (srenderType != null && !srenderType.equals("")) { try { RenderType renderType = RenderType.valueOf(srenderType); dom.getController().getPlotElement().setRenderType(renderType); } catch (IllegalArgumentException ex) { ex.printStackTrace(); } } System.err.println("done setRenderType @ " + (System.currentTimeMillis() - t0) + " msec"); if (!scolor.equals("")) { try { dom.getController().getPlotElement().getStyle().setColor(Color.decode(scolor)); } catch (Exception ex) { ex.printStackTrace(); } } if (!sfillColor.equals("")) { try { dom.getController().getPlotElement().getStyle().setFillColor(Color.decode(sfillColor)); } catch (Exception ex) { ex.printStackTrace(); } } if (!sforegroundColor.equals("")) { try { dom.getOptions().setForeground(Color.decode(sforegroundColor)); } catch (Exception ex) { ex.printStackTrace(); } } if (!sbackgroundColor.equals("")) { try { dom.getOptions().setBackground(Color.decode(sbackgroundColor)); } catch (Exception ex) { ex.printStackTrace(); } } surl = getParameter("dataSetURL"); if (surl != null) { if (surl.startsWith("about:")) { setDataSetURL(surl); } else { } } getContentPane().remove(progressComponent); getContentPane().add(model.getCanvas()); System.err.println("done add to applet @ " + (System.currentTimeMillis() - t0) + " msec"); validate(); System.err.println("done applet.validate @ " + (System.currentTimeMillis() - t0) + " msec"); repaint(); appmodel.getCanvas().setVisible(true); initializing = false; repaint(); System.err.println("ready @ " + (System.currentTimeMillis() - t0) + " msec"); setInitializationStatus("ready"); dom.getController().getPlot().getXaxis().addPropertyChangeListener(Axis.PROP_RANGE, new PropertyChangeListener() { public void propertyChange(PropertyChangeEvent evt) { timeCallback(String.valueOf(evt.getNewValue())); } }); if (!clickCallback.equals("")) { String clickCallbackLabel = "Applet Click"; int i = clickCallback.indexOf(","); if (i != -1) { int i2 = clickCallback.indexOf("label="); if (i2 != -1) clickCallbackLabel = clickCallback.substring(i2 + 6).trim(); clickCallback = clickCallback.substring(0, i).trim(); } final DasPlot plot = dom.getPlots(0).getController().getDasPlot(); MouseModule mm = new MouseModule(plot, new CrossHairRenderer(plot, null, plot.getXAxis(), plot.getYAxis()), clickCallbackLabel) { @Override public void mousePressed(MouseEvent e) { e = SwingUtilities.convertMouseEvent(plot, e, plot.getCanvas()); clickCallback(dom.getPlots(0).getId(), plot, e); } @Override public void mouseDragged(MouseEvent e) { e = SwingUtilities.convertMouseEvent(plot, e, plot.getCanvas()); clickCallback(dom.getPlots(0).getId(), plot, e); } @Override public void mouseReleased(MouseEvent e) { e = SwingUtilities.convertMouseEvent(plot, e, plot.getCanvas()); clickCallback(dom.getPlots(0).getId(), plot, e); } }; plot.getDasMouseInputAdapter().setPrimaryModule(mm); } p.getController().getDasPlot().getDasMouseInputAdapter().removeMenuItem("Properties"); dom.getPlots(0).getXaxis().getController().getDasAxis().getDasMouseInputAdapter().removeMenuItem("Properties"); dom.getPlots(0).getYaxis().getController().getDasAxis().getDasMouseInputAdapter().removeMenuItem("Properties"); dom.getPlots(0).getZaxis().getController().getDasAxis().getDasMouseInputAdapter().removeMenuItem("Properties"); if (getStringParameter("contextOverview", "off").equals("on")) { Runnable run = new Runnable() { public void run() { dom.getController().waitUntilIdle(); try { Thread.sleep(100); } catch (InterruptedException ex) { Logger.getLogger(AutoplotApplet.class.getName()).log(Level.SEVERE, null, ex); } dom.getController().waitUntilIdle(); doSetOverview(true); } }; new Thread(run).start(); } System.err.println("done start AutoplotApplet " + VERSION + " @ " + (System.currentTimeMillis() - t0) + " msec"); } | protected void copyFile(String from, String to, String workingDirectory) throws Exception { URL monitorCallShellScriptUrl = Thread.currentThread().getContextClassLoader().getResource(from); File f = new File(monitorCallShellScriptUrl.getFile()); String directoryPath = f.getAbsolutePath(); String fileName = from; InputStream in = null; if (directoryPath.indexOf(".jar!") > -1) { URL urlJar = new URL(directoryPath.substring(directoryPath.indexOf("file:"), directoryPath.indexOf('!'))); JarFile jf = new JarFile(urlJar.getFile()); JarEntry je = jf.getJarEntry(from); fileName = je.getName(); in = Thread.currentThread().getContextClassLoader().getResourceAsStream(fileName); } else { in = new FileInputStream(f); } File outScriptFile = new File(to); FileOutputStream fos = new FileOutputStream(outScriptFile); int nextChar; while ((nextChar = in.read()) != -1) fos.write(nextChar); fos.flush(); fos.close(); try { LinuxCommandExecutor cmdExecutor = new LinuxCommandExecutor(); cmdExecutor.setWorkingDirectory(workingDirectory); cmdExecutor.runCommand("chmod 777 " + to); } catch (Exception e) { throw e; } } | 885,797 |
1 | public static void compress(final File zip, final Map<InputStream, String> entries, final IProgressMonitor monitor) throws IOException { if (zip == null || entries == null || CollectionUtils.isEmpty(entries.keySet())) throw new IllegalArgumentException("One ore more parameters are empty!"); if (zip.exists()) zip.delete(); else if (!zip.getParentFile().exists()) zip.getParentFile().mkdirs(); ZipOutputStream out = new ZipOutputStream(new BufferedOutputStream(new FileOutputStream(zip))); out.setLevel(Deflater.BEST_COMPRESSION); try { for (InputStream inputStream : entries.keySet()) { ZipEntry zipEntry = new ZipEntry(skipBeginningSlash(entries.get(inputStream))); out.putNextEntry(zipEntry); IOUtils.copy(inputStream, out); out.closeEntry(); inputStream.close(); if (monitor != null) monitor.worked(1); } } finally { IOUtils.closeQuietly(out); } } | public void filter(File source, File destination, MNamespace mNamespace) throws Exception { BufferedReader reader = new BufferedReader(new FileReader(source)); BufferedWriter writer = new BufferedWriter(new FileWriter(destination)); int line = 0; int column = 0; Stack parseStateStack = new Stack(); parseStateStack.push(new ParseState(mNamespace)); for (Iterator i = codePieces.iterator(); i.hasNext(); ) { NamedCodePiece cp = (NamedCodePiece) i.next(); while (line < cp.getStartLine()) { line++; column = 0; writer.write(reader.readLine()); writer.newLine(); } while (column < cp.getStartPosition()) { writer.write(reader.read()); column++; } cp.write(writer, parseStateStack, column); while (line < cp.getEndLine()) { line++; column = 0; reader.readLine(); } while (column < cp.getEndPosition()) { column++; reader.read(); } } String data; while ((data = reader.readLine()) != null) { writer.write(data); writer.newLine(); } reader.close(); writer.close(); } | 885,798 |
1 | private static void copy(String srcFilename, String dstFilename, boolean override) throws IOException, XPathFactoryConfigurationException, SAXException, ParserConfigurationException, XPathExpressionException { File fileToCopy = new File(rootDir + "test-output/" + srcFilename); if (fileToCopy.exists()) { File newFile = new File(rootDir + "test-output/" + dstFilename); if (!newFile.exists() || override) { try { FileChannel srcChannel = new FileInputStream(rootDir + "test-output/" + srcFilename).getChannel(); FileChannel dstChannel = new FileOutputStream(rootDir + "test-output/" + dstFilename).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException e) { } } } } | public static void copyFile(File sourceFile, File destFile) throws IOException { if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { if (source != null) { source.close(); } if (destination != null) { destination.close(); } } } | 885,799 |
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