List of usage examples for java.io IOException getStackTrace
public StackTraceElement[] getStackTrace()
From source file:com.bah.applefox.main.plugins.pageranking.utilities.PRtoFile.java
private static HashMap<String, Double> createMap(String[] args) throws AccumuloException, AccumuloSecurityException, TableNotFoundException { HashMap<String, Double> ret = new HashMap<String, Double>(); String readTable = args[13] + "Old"; Scanner scan = AccumuloUtils.connectRead(readTable); Iterator<Entry<Key, Value>> itr = scan.iterator(); while (itr.hasNext()) { Entry<Key, Value> temp = itr.next(); try {/*from w w w.ja v a 2s. c o m*/ Double val = (Double) IngestUtils.deserialize(temp.getValue().get()); ret.put(temp.getKey().getRow().toString(), val); System.out.println("Adding to Map: " + temp.getKey().getRow().toString() + " with rank: " + val); } catch (IOException e) { if (e.getMessage() != null) { log.error(e.getMessage()); } else { log.error(e.getStackTrace()); } } catch (ClassNotFoundException e) { if (e.getMessage() != null) { log.error(e.getMessage()); } else { log.error(e.getStackTrace()); } } } Double max = 0.0; Collection<Double> values = ret.values(); ArrayList<Double> tempValues = new ArrayList<Double>(); tempValues.addAll(values); Collections.sort(tempValues); Collections.reverse(tempValues); max = tempValues.get(0); ret.put("[[MAX_PR]]", max); return ret; }
From source file:br.pucminas.ri.jsearch.rest.controller.ApiController.java
private static IndexerResponse performIndex() { IndexerResponse res;//from w w w .j a v a2 s .c o m try { res = Indexer.performIndex(); } catch (IOException ex) { res = new IndexerResponse(); res.setError(true); System.out.println(Arrays.toString(ex.getStackTrace())); } return res; }
From source file:com.catalyst.sonar.score.batch.util.FileInstaller.java
/** * Copies bytes from an InputStream to an OutputStream. * //from w w w. ja v a 2s . c o m * @param is * @param os * @return true if copy is successful, false otherwise. */ private static boolean copyStream(final InputStream is, final OutputStream os) { logger.debug("copyStream(InputStream is, OutputStream os)"); boolean success = false; try { final byte[] buf = new byte[1024]; int len = 0; while ((len = is.read(buf)) > 0) { os.write(buf, 0, len); } is.close(); os.close(); success = true; logger.debug("returning " + success); return success; } catch (final IOException e) { logger.debug(e.getStackTrace().toString()); } logger.debug("returning " + success); return false; }
From source file:net.sf.taverna.t2.security.credentialmanager.impl.CredentialManagerImplIT.java
@AfterClass @Ignore/*from www . j av a 2 s .co m*/ // Clean up the credentialManagerDirectory we created for testing public static void cleanUp() { if (credentialManagerDirectory.exists()) { try { FileUtils.deleteDirectory(credentialManagerDirectory); System.out.println( "Deleting Credential Manager's directory: " + credentialManagerDirectory.getAbsolutePath()); } catch (IOException e) { System.out.println(e.getStackTrace()); } } }
From source file:com.github.rcaller.util.RCodeUtils.java
public static void addDataFrame(StringBuffer rCode, String name, DataFrame dataFrame) { try {//from w w w . j av a 2s . c o m File file = File.createTempFile("dataFrame", ".csv"); CSVFileWriter csvFileWriter = CSVFileWriter.create(file.getAbsolutePath()); csvFileWriter.writeDataFrameToFile(dataFrame); rCode.append(name).append(" <- read.csv(\"").append(file.getAbsolutePath()).append("\")\n"); } catch (IOException e) { Logger.getLogger(RCodeUtils.class.getName()).log(Level.WARNING, "Couldn't export data frame to csv-file!", e.getStackTrace()); } }
From source file:org.sherlok.utils.SherlokTests.java
public static Map<String, List<JsonAnnotation>> assertEquals(Map<String, List<JsonAnnotation>> expecteds, String actualsString, Comparison comparison) throws SherlokException, JSONException, JsonProcessingException { // parse/*from w w w .ja va 2s . com*/ Map<String, List<JsonAnnotation>> actuals = null; try { actuals = SherlokResult.parse(actualsString).getAnnotations(); } catch (IOException e) { throw new SherlokException("could not parse actual annotations").setObject(actualsString) .setDetails(e.getStackTrace()); } // validate switch (comparison) { case atLeast: // For each annotation in expecteds we make sure it exists in // actuals for (Entry<String, List<JsonAnnotation>> entry : expecteds.entrySet()) { String expectedAnnotationClass = entry.getKey(); List<JsonAnnotation> expectedAnnotations = entry.getValue(); // Get the corresponding annotations and make sure they exists List<JsonAnnotation> actualValues = actuals.get(expectedAnnotationClass); if (actualValues == null) { throw new SherlokException("could not find expected Annotations of type '" + expectedAnnotationClass + "', could only find Annotations of type '" + join(actuals.keySet(), "', '") + "'", expectedAnnotationClass)// .setDetails(map("expected", expecteds, "actual", actuals)); } for (JsonAnnotation expected : expectedAnnotations) { // Find an annotation that has the same begin and end in the // actual annotations. Note that two annotations with the // same key and same region are not supported by this test. JsonAnnotation actual = null; for (JsonAnnotation annotation : actualValues) { if (expected.getBegin() == annotation.getBegin() && expected.getEnd() == annotation.getEnd()) { actual = annotation; break; } } // Make sure that such (begin, end) pair was found if (actual == null) { throw new SherlokException("could not find expected annotation " + expectedAnnotationClass + expected.toString(), expected.toString())// .setDetails(map("expected", expecteds, "actual", actuals)); } // Make sure that each expected properties exist Map<String, Object> expectedProperties = expected.getProperties(); Map<String, Object> actualProperties = actual.getProperties(); for (Entry<String, Object> expectedProperty : expectedProperties.entrySet()) { Object actualProperty = actualProperties.get(expectedProperty.getKey()); // This isn't a proper recursive solution: it means // that sub-properties must be included in both // expected and actual properties. Hence the "at least" // test is not perfect. if (!expectedProperty.getValue().equals(actualProperty)) { throw new SherlokException("actual property '" + actualProperty + "' is not equal to expected property '" + expectedProperty + "'")// .setDetails(map("expected", expecteds, "actual", actuals)); } } } } break; case exact:// FIXME implement exact comparison for (Entry<String, List<JsonAnnotation>> exp : expecteds.entrySet()) { String eType = exp.getKey(); if (!actuals.containsKey(eType)) { throw new SherlokException("could not find expected key", eType); } else { for (JsonAnnotation a : exp.getValue()) { boolean found = false; for (JsonAnnotation sa : actuals.get(eType)) { // FIXME currently it is not recursive if (sa.equals(a)) { found = true; break; } } if (!found) { throw new SherlokException("could not find expected annotation", a.toString()); } } } } break; /*- // compare 2-ways; give explicit error msg for (Entry<String, List<Annotation>> exp : expecteds.entrySet()) { if (!systems.values().contains(exp)) { throw new SherlokException(map(ERR_NOTFOUND, exp, EXPECTED, expecteds, SYSTEM, systems)); } } for (List<Annotation> sysAs : systems.values()) { for (Annotation sysa : sysAs) { if (!expecteds.values().contains(sysa)) { throw new SherlokException(map(ERR_UNEXPECTED, sysa, EXPECTED, expecteds, SYSTEM, systems)); } } } break; */ } return actuals; }
From source file:uk.ac.ucl.chem.ccs.clinicalgui.ClinicalGuiClient.java
private static void loadProperties() { String confprop = System.getProperty("uk.ac.ucl.chem.ccs.aheclient.conffile"); if (confprop != null && !confprop.equals("")) { propertiesFile = confprop;/* w ww. jav a 2 s . com*/ System.out.println("foo" + propertiesFile); } else { propertiesFile = "aheclient.properties"; } prop = new Properties(); try { prop.load(new FileInputStream(propertiesFile)); cat.info("Opened properties file " + propertiesFile); } catch (IOException e) { cat.error("Couldn't open properties file " + propertiesFile + "!"); cat.error(e.getMessage()); cat.debug(e.getStackTrace()); cat.error("Configure client settings now"); prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.myproxy-server", "myproxy.grid-support.ac.uk"); prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.myproxy-dn", "/C=UK/O=eScience/OU=CLRC/L=DL/CN=host/myproxy.grid-support.ac.uk/E=a.j.richards@dl.ac.uk"); prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.myproxy-port", "7512"); prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.myproxy-lifetime", "7512"); prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.myproxy-un", ""); prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.myproxy-pw", ""); prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.ahedavuser", ""); prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.ahedavpasswd", ""); prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.ahedavserver", ""); prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.jobregepr", ""); prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.keystore", "aheclient.ks"); prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.jobfactoryepr", ""); prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.mpcheck", "false"); prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.mpwarn", "false"); //some more //proxy location prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.proxyfile", "/tmp/x501"); //gridftp server prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.gridftpserver", "none"); //gridftp port prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.gridftpport", "2811"); //repository location prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.modelrep", "/models"); //dicom server prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.dicomserver", "none"); prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.dicomserverport", "none"); //dicom client prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.dicomclient", "none"); prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.dicomclientport", "none"); //dicom client name prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.dicomclientname", "false"); //dicom tempdir prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.dicomtmpdir", "/tmp"); //dicom slices prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.dicomslices", "/tmp"); //harc-path prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.harcpath", "false"); //harc-path prop.setProperty("uk.ac.ucl.chem.ccs.aheclient.segtool", "/tmp/sg"); } //set HARC client properties from file to system properties System.setProperty("harc.client.installpath", prop.getProperty("uk.ac.ucl.chem.ccs.aheclient.harcpath")); System.setProperty("harc.client.secure.gsi_proxy_location", prop.getProperty("uk.ac.ucl.chem.ccs.aheclient.proxyfile")); System.setProperty("ahe.java.version", prop.getProperty("uk.ac.ucl.chem.ccs.aheclient.javaversion")); //unlock String passwd = null; passwd = prop.getProperty("uk.ac.ucl.chem.ccs.aheclient.passwd"); if (!checkKeystore(passwd)) { System.err.println("Can't open keystore"); } }
From source file:eu.eco2clouds.api.bonfire.client.rest.RestClient.java
private static Response executeMethod(HttpMethod httpMethod, String type, String username, String password, String url) {//from w ww. j ava 2 s. c o m HttpClient client = getClient(url, username, password); Response response = null; // We set the Heathers httpMethod.setDoAuthentication(true); httpMethod.addRequestHeader(BONFIRE_ASSERTED_ID_HEADER, username); //httpMethod.addRequestHeader(BONFIRE_ASSERTED_ID_HEADER, groups); httpMethod.addRequestHeader("Accept", type); httpMethod.addRequestHeader("Content-Type", type); try { int statusCode = client.executeMethod(httpMethod); String responsePayload = httpMethod.getResponseBodyAsString(); response = new Response(statusCode, responsePayload); } catch (IOException iOException) { System.out.println("ERROR TRYING TO PERFORM GET TO: " + httpMethod.getPath()); System.out.println("ERROR: " + iOException.getMessage()); System.out.println("ERROR: " + iOException.getStackTrace()); } finally { httpMethod.releaseConnection(); } return response; }
From source file:com.jktsoftware.amazondownloader.download.Application.java
public static void downloadObject(IObject objecttodownload, IQueueManager queuemanager) { ConsoleProgressBar progressbar = new ConsoleProgressBar(); System.out.println("Attempting to get object: " + objecttodownload.getObjectKey()); try {//from w w w . ja va2 s. c o m //create an inputstream object for the download from the repo InputStream input = objecttodownload.getObjectContent(); //create an outputstream for writing the stream to a local file OutputStream outStream = new FileOutputStream(objecttodownload.getObjectKey()); //current bytes read from the repo long currentbytes = 0; //bytes read within the loop int bytesread = 0; //print status message to the console System.out.println("Starting download of :" + objecttodownload.getObjectKey()); //progress message variable String previousprogress = ""; //buffer for holding downloaded bytes byte[] bytebuffer = new byte[512 * 1024]; //start downloading file bit by bit while ((bytesread = input.read(bytebuffer)) != -1) { //write downloaded bytes to the file outStream.write(bytebuffer, 0, bytesread); //update downloaded byte count currentbytes = currentbytes + bytesread; //get a text representation of a progress bar String newprogress = progressbar.getProgress(currentbytes, objecttodownload.getObjectSize()) + "\r"; if (!newprogress.contentEquals(previousprogress)) { //write progress bar to console System.out.print(newprogress); previousprogress = newprogress; } } //write progress bar to console System.out.println(progressbar.getProgress(currentbytes, objecttodownload.getObjectSize())); System.out.println("Object downloaded"); //close the streams input.close(); outStream.close(); //update queue with details of downloaded file queuemanager.sendReceivedObjectMessageToQueue(objecttodownload.getObjectKey()); } catch (IOException e) { e.printStackTrace(); //update queue with details of failed file queuemanager.sendFailedObjectMessageToQueue(objecttodownload.getObjectKey(), e.getStackTrace().toString()); } }
From source file:de.ingrid.iplug.csw.dsc.tools.FileUtils.java
/** * This function will copy files or directories from one location to another. * note that the source and the destination must be mutually exclusive. This * function can not be used to copy a directory to a sub directory of itself. * The function will also have problems if the destination files already exist. * @param src -- A File object that represents the source for the copy * @param dest -- A File object that represnts the destination for the copy. * @throws IOException if unable to copy. * /*from w w w.j av a 2 s.c o m*/ * Source: http://www.dreamincode.net/code/snippet1443.htm */ public static void copyRecursive(File src, File dest) throws IOException { //Check to ensure that the source is valid... if (!src.exists()) { throw new IOException("copyFiles: Can not find source: " + src.getAbsolutePath() + "."); } else if (!src.canRead()) { //check to ensure we have rights to the source... throw new IOException("copyFiles: No right to source: " + src.getAbsolutePath() + "."); } //is this a directory copy? if (src.isDirectory()) { if (!dest.exists()) { //does the destination already exist? //if not we need to make it exist if possible (note this is mkdirs not mkdir) if (!dest.mkdirs()) { throw new IOException("copyFiles: Could not create direcotry: " + dest.getAbsolutePath() + "."); } } //get a listing of files... String list[] = src.list(); //copy all the files in the list. for (int i = 0; i < list.length; i++) { File dest1 = new File(dest, list[i]); File src1 = new File(src, list[i]); copyRecursive(src1, dest1); } } else { //This was not a directory, so lets just copy the file FileInputStream fin = null; FileOutputStream fout = null; byte[] buffer = new byte[4096]; //Buffer 4K at a time (you can change this). int bytesRead; try { //open the files for input and output fin = new FileInputStream(src); fout = new FileOutputStream(dest); //while bytesRead indicates a successful read, lets write... while ((bytesRead = fin.read(buffer)) >= 0) { fout.write(buffer, 0, bytesRead); } fin.close(); fout.close(); fin = null; fout = null; } catch (IOException e) { //Error copying file... IOException wrapper = new IOException("copyFiles: Unable to copy file: " + src.getAbsolutePath() + "to" + dest.getAbsolutePath() + "."); wrapper.initCause(e); wrapper.setStackTrace(e.getStackTrace()); throw wrapper; } finally { //Ensure that the files are closed (if they were open). if (fin != null) { fin.close(); } if (fout != null) { fin.close(); } } } }