List of usage examples for org.apache.commons.httpclient.methods GetMethod GetMethod
public GetMethod(String uri)
From source file:com.djimenez.tuenti.example.FormLoginDemo.java
public static void main(final String[] args) throws Exception { final HttpClient client = new HttpClient(); client.getHostConfiguration().setHost(LOGON_SITE, LOGON_PORT, "http"); client.getParams().setCookiePolicy(CookiePolicy.BROWSER_COMPATIBILITY); // 'developer.java.sun.com' has cookie compliance problems // Their session cookie's domain attribute is in violation of the RFC2109 // We have to resort to using compatibility cookie policy final GetMethod authget = new GetMethod(LOGON_PATH); authget.setFollowRedirects(true);/*from w ww. jav a 2s.co m*/ client.executeMethod(authget); System.out.println("Login form get: " + authget.getStatusLine().toString()); // release any connection resources used by the method authget.releaseConnection(); // See if we got any cookies final CookieSpec cookiespec = CookiePolicy.getDefaultSpec(); final Cookie[] initcookies = cookiespec.match(LOGON_SITE, LOGON_PORT, "/", false, client.getState().getCookies()); System.out.println("Initial set of cookies:"); checkCookies(initcookies); final PostMethod authpost = new PostMethod(LOGON_PATH); // Prepare login parameters final NameValuePair action = new NameValuePair("action", "do_login"); final NameValuePair url = new NameValuePair("url", "/?m=Login&func=do_login"); final NameValuePair userid = new NameValuePair("email", "david.jimenez19%40gmail.com"); final NameValuePair password = new NameValuePair("input_password", "linda1"); final NameValuePair timeZone = new NameValuePair("timezone", "1"); final NameValuePair timeStamp = new NameValuePair("timezone", "13034395121"); authpost.setRequestBody(new NameValuePair[] { action, url, userid, password, timeZone, timeStamp }); client.executeMethod(authpost); System.out.println("Login form post: " + authpost.getStatusLine().toString()); // release any connection resources used by the method authpost.releaseConnection(); // See if we got any cookies // The only way of telling whether logon succeeded is // by finding a session cookie final Cookie[] logoncookies = cookiespec.match(LOGON_SITE, LOGON_PORT, "/", false, client.getState().getCookies()); System.out.println("Logon cookies:" + logoncookies); checkCookies(logoncookies); manageRequest(client, authpost); }
From source file:CookieDemoApp.java
/** * * Usage://w w w .jav a2 s .c o m * java CookieDemoApp http://mywebserver:80/ * * @param args command line arguments * Argument 0 is a URL to a web server * * */ public static void main(String[] args) throws Exception { if (args.length != 1) { System.err.println("Usage: java CookieDemoApp <url>"); System.err.println("<url> The url of a webpage"); System.exit(1); } // Get target URL String strURL = args[0]; System.out.println("Target URL: " + strURL); // Get initial state object HttpState initialState = new HttpState(); // Initial set of cookies can be retrieved from persistent storage and // re-created, using a persistence mechanism of choice, Cookie mycookie = new Cookie(".foobar.com", "mycookie", "stuff", "/", null, false); // and then added to your HTTP state instance initialState.addCookie(mycookie); // Get HTTP client instance HttpClient httpclient = new HttpClient(); httpclient.getHttpConnectionManager().getParams().setConnectionTimeout(30000); httpclient.setState(initialState); // RFC 2101 cookie management spec is used per default // to parse, validate, format & match cookies httpclient.getParams().setCookiePolicy(CookiePolicy.RFC_2109); // A different cookie management spec can be selected // when desired //httpclient.getParams().setCookiePolicy(CookiePolicy.NETSCAPE); // Netscape Cookie Draft spec is provided for completeness // You would hardly want to use this spec in real life situations //httppclient.getParams().setCookiePolicy(CookiePolicy.BROWSER_COMPATIBILITY); // Compatibility policy is provided in order to mimic cookie // management of popular web browsers that is in some areas // not 100% standards compliant // Get HTTP GET method GetMethod httpget = new GetMethod(strURL); // Execute HTTP GET int result = httpclient.executeMethod(httpget); // Display status code System.out.println("Response status code: " + result); // Get all the cookies Cookie[] cookies = httpclient.getState().getCookies(); // Display the cookies System.out.println("Present cookies: "); for (int i = 0; i < cookies.length; i++) { System.out.println(" - " + cookies[i].toExternalForm()); } // Release current connection to the connection pool once you are done httpget.releaseConnection(); }
From source file:ExampleP2PHttpClient.java
public static void main(String[] args) { // initialize JXTA try {//from www . j av a2s .co m // sign in and initialize the JXTA network; profile this peer and create it // if it doesn't exist P2PNetwork.signin("clientpeer", "clientpeerpassword", "TestNetwork", true); } catch (Exception e) { e.printStackTrace(); System.exit(1); } // register the P2P socket protocol factory Protocol jxtaHttp = new Protocol("p2phttp", new P2PProtocolSocketFactory(), 80); Protocol.registerProtocol("p2phttp", jxtaHttp); //create a singular HttpClient object HttpClient client = new HttpClient(); //establish a connection within 50 seconds client.setConnectionTimeout(50000); String url = System.getProperty("url"); if (url == null || url.equals("")) { System.out.println("You must provide a URL to access. For example:"); System.out.println("ant example-webclient-run -D--url=p2phttp://www.somedomain.foo"); System.exit(1); } System.out.println("Connecting to " + url + "..."); HttpMethod method = null; //create a method object method = new GetMethod(url); method.setFollowRedirects(true); method.setStrictMode(false); //} catch (MalformedURLException murle) { // System.out.println("<url> argument '" + url // + "' is not a valid URL"); // System.exit(-2); //} //execute the method String responseBody = null; try { client.executeMethod(method); responseBody = method.getResponseBodyAsString(); } catch (HttpException he) { System.err.println("Http error connecting to '" + url + "'"); System.err.println(he.getMessage()); System.exit(-4); } catch (IOException ioe) { System.err.println("Unable to connect to '" + url + "'"); System.exit(-3); } //write out the request headers System.out.println("*** Request ***"); System.out.println("Request Path: " + method.getPath()); System.out.println("Request Query: " + method.getQueryString()); Header[] requestHeaders = method.getRequestHeaders(); for (int i = 0; i < requestHeaders.length; i++) { System.out.print(requestHeaders[i]); } //write out the response headers System.out.println("*** Response ***"); System.out.println("Status Line: " + method.getStatusLine()); Header[] responseHeaders = method.getResponseHeaders(); for (int i = 0; i < responseHeaders.length; i++) { System.out.print(responseHeaders[i]); } //write out the response body System.out.println("*** Response Body ***"); System.out.println(responseBody); //clean up the connection resources method.releaseConnection(); method.recycle(); System.exit(0); }
From source file:com.cloud.test.utils.TestClient.java
public static void main(String[] args) { String host = "http://localhost"; String port = "8080"; String testUrl = "/client/test"; int numThreads = 1; try {/* w ww . j a va2 s . c om*/ // Parameters List<String> argsList = Arrays.asList(args); Iterator<String> iter = argsList.iterator(); while (iter.hasNext()) { String arg = iter.next(); // host if (arg.equals("-h")) { host = "http://" + iter.next(); } if (arg.equals("-p")) { port = iter.next(); } if (arg.equals("-t")) { numThreads = Integer.parseInt(iter.next()); } if (arg.equals("-s")) { sleepTime = Long.parseLong(iter.next()); } if (arg.equals("-c")) { cleanUp = Boolean.parseBoolean(iter.next()); if (!cleanUp) sleepTime = 0L; // no need to wait if we don't ever cleanup } if (arg.equals("-r")) { repeat = Boolean.parseBoolean(iter.next()); } if (arg.equals("-u")) { numOfUsers = Integer.parseInt(iter.next()); } if (arg.equals("-i")) { internet = Boolean.parseBoolean(iter.next()); } } final String server = host + ":" + port + testUrl; s_logger.info("Starting test against server: " + server + " with " + numThreads + " thread(s)"); if (cleanUp) s_logger.info("Clean up is enabled, each test will wait " + sleepTime + " ms before cleaning up"); if (numOfUsers > 0) { s_logger.info("Pre-generating users for test of size : " + numOfUsers); users = new String[numOfUsers]; Random ran = new Random(); for (int i = 0; i < numOfUsers; i++) { users[i] = Math.abs(ran.nextInt()) + "-user"; } } for (int i = 0; i < numThreads; i++) { new Thread(new Runnable() { public void run() { do { String username = null; try { long now = System.currentTimeMillis(); Random ran = new Random(); if (users != null) { username = users[Math.abs(ran.nextInt()) % numOfUsers]; } else { username = Math.abs(ran.nextInt()) + "-user"; } NDC.push(username); String url = server + "?email=" + username + "&password=" + username + "&command=deploy"; s_logger.info("Launching test for user: " + username + " with url: " + url); HttpClient client = new HttpClient(); HttpMethod method = new GetMethod(url); int responseCode = client.executeMethod(method); boolean success = false; String reason = null; if (responseCode == 200) { if (internet) { s_logger.info("Deploy successful...waiting 5 minute before SSH tests"); Thread.sleep(300000L); // Wait 60 seconds so the linux VM can boot up. s_logger.info("Begin Linux SSH test"); reason = sshTest(method.getResponseHeader("linuxIP").getValue()); if (reason == null) { s_logger.info("Linux SSH test successful"); s_logger.info("Begin Windows SSH test"); reason = sshWinTest(method.getResponseHeader("windowsIP").getValue()); } } if (reason == null) { if (internet) { s_logger.info("Windows SSH test successful"); } else { s_logger.info("deploy test successful....now cleaning up"); if (cleanUp) { s_logger.info( "Waiting " + sleepTime + " ms before cleaning up vms"); Thread.sleep(sleepTime); } else { success = true; } } if (users == null) { s_logger.info("Sending cleanup command"); url = server + "?email=" + username + "&password=" + username + "&command=cleanup"; } else { s_logger.info("Sending stop DomR / destroy VM command"); url = server + "?email=" + username + "&password=" + username + "&command=stopDomR"; } method = new GetMethod(url); responseCode = client.executeMethod(method); if (responseCode == 200) { success = true; } else { reason = method.getStatusText(); } } else { // Just stop but don't destroy the VMs/Routers s_logger.info("SSH test failed with reason '" + reason + "', stopping VMs"); url = server + "?email=" + username + "&password=" + username + "&command=stop"; responseCode = client.executeMethod(new GetMethod(url)); } } else { // Just stop but don't destroy the VMs/Routers reason = method.getStatusText(); s_logger.info("Deploy test failed with reason '" + reason + "', stopping VMs"); url = server + "?email=" + username + "&password=" + username + "&command=stop"; client.executeMethod(new GetMethod(url)); } if (success) { s_logger.info("***** Completed test for user : " + username + " in " + ((System.currentTimeMillis() - now) / 1000L) + " seconds"); } else { s_logger.info("##### FAILED test for user : " + username + " in " + ((System.currentTimeMillis() - now) / 1000L) + " seconds with reason : " + reason); } } catch (Exception e) { s_logger.warn("Error in thread", e); try { HttpClient client = new HttpClient(); String url = server + "?email=" + username + "&password=" + username + "&command=stop"; client.executeMethod(new GetMethod(url)); } catch (Exception e1) { } } finally { NDC.clear(); } } while (repeat); } }).start(); } } catch (Exception e) { s_logger.error(e); } }
From source file:com.cloud.sample.UserCloudAPIExecutor.java
public static void main(String[] args) { // Host//from w ww . j a v a 2 s .c o m String host = null; // Fully qualified URL with http(s)://host:port String apiUrl = null; // ApiKey and secretKey as given by your CloudStack vendor String apiKey = null; String secretKey = null; try { Properties prop = new Properties(); prop.load(new FileInputStream("usercloud.properties")); // host host = prop.getProperty("host"); if (host == null) { System.out.println( "Please specify a valid host in the format of http(s)://:/client/api in your usercloud.properties file."); } // apiUrl apiUrl = prop.getProperty("apiUrl"); if (apiUrl == null) { System.out.println( "Please specify a valid API URL in the format of command=¶m1=¶m2=... in your usercloud.properties file."); } // apiKey apiKey = prop.getProperty("apiKey"); if (apiKey == null) { System.out.println( "Please specify your API Key as provided by your CloudStack vendor in your usercloud.properties file."); } // secretKey secretKey = prop.getProperty("secretKey"); if (secretKey == null) { System.out.println( "Please specify your secret Key as provided by your CloudStack vendor in your usercloud.properties file."); } if (apiUrl == null || apiKey == null || secretKey == null) { return; } System.out.println("Constructing API call to host = '" + host + "' with API command = '" + apiUrl + "' using apiKey = '" + apiKey + "' and secretKey = '" + secretKey + "'"); // Step 1: Make sure your APIKey is URL encoded String encodedApiKey = URLEncoder.encode(apiKey, "UTF-8"); // Step 2: URL encode each parameter value, then sort the parameters and apiKey in // alphabetical order, and then toLowerCase all the parameters, parameter values and apiKey. // Please note that if any parameters with a '&' as a value will cause this test client to fail since we are using // '&' to delimit // the string List<String> sortedParams = new ArrayList<String>(); sortedParams.add("apikey=" + encodedApiKey.toLowerCase()); StringTokenizer st = new StringTokenizer(apiUrl, "&"); String url = null; boolean first = true; while (st.hasMoreTokens()) { String paramValue = st.nextToken(); String param = paramValue.substring(0, paramValue.indexOf("=")); String value = URLEncoder .encode(paramValue.substring(paramValue.indexOf("=") + 1, paramValue.length()), "UTF-8"); if (first) { url = param + "=" + value; first = false; } else { url = url + "&" + param + "=" + value; } sortedParams.add(param.toLowerCase() + "=" + value.toLowerCase()); } Collections.sort(sortedParams); System.out.println("Sorted Parameters: " + sortedParams); // Step 3: Construct the sorted URL and sign and URL encode the sorted URL with your secret key String sortedUrl = null; first = true; for (String param : sortedParams) { if (first) { sortedUrl = param; first = false; } else { sortedUrl = sortedUrl + "&" + param; } } System.out.println("sorted URL : " + sortedUrl); String encodedSignature = signRequest(sortedUrl, secretKey); // Step 4: Construct the final URL we want to send to the CloudStack Management Server // Final result should look like: // http(s)://://client/api?&apiKey=&signature= String finalUrl = host + "?" + url + "&apiKey=" + apiKey + "&signature=" + encodedSignature; System.out.println("final URL : " + finalUrl); // Step 5: Perform a HTTP GET on this URL to execute the command HttpClient client = new HttpClient(); HttpMethod method = new GetMethod(finalUrl); int responseCode = client.executeMethod(method); if (responseCode == 200) { // SUCCESS! System.out.println("Successfully executed command"); } else { // FAILED! System.out.println("Unable to execute command with response code: " + responseCode); } } catch (Throwable t) { System.out.println(t); } }
From source file:com.era7.bioinfo.annotation.AutomaticQualityControl.java
public static void main(String[] args) { if (args.length != 4) { System.out.println("This program expects four parameters: \n" + "1. Gene annotation XML filename \n" + "2. Reference protein set (.fasta)\n" + "3. Output TXT filename\n" + "4. Initial Blast XML results filename (the one used at the very beginning of the semiautomatic annotation process)\n"); } else {/*from ww w . j a v a 2 s . co m*/ BufferedWriter outBuff = null; try { File inFile = new File(args[0]); File fastaFile = new File(args[1]); File outFile = new File(args[2]); File blastFile = new File(args[3]); //Primero cargo todos los datos del archivo xml del blast BufferedReader buffReader = new BufferedReader(new FileReader(blastFile)); StringBuilder stBuilder = new StringBuilder(); String line = null; while ((line = buffReader.readLine()) != null) { stBuilder.append(line); } buffReader.close(); System.out.println("Creating blastoutput..."); BlastOutput blastOutput = new BlastOutput(stBuilder.toString()); System.out.println("BlastOutput created! :)"); stBuilder.delete(0, stBuilder.length()); HashMap<String, String> blastProteinsMap = new HashMap<String, String>(); ArrayList<Iteration> iterations = blastOutput.getBlastOutputIterations(); for (Iteration iteration : iterations) { blastProteinsMap.put(iteration.getQueryDef().split("\\|")[1].trim(), iteration.toString()); } //freeing some memory blastOutput = null; //------------------------------------------------------------------------ //Initializing writer for output file outBuff = new BufferedWriter(new FileWriter(outFile)); //reading gene annotation xml file..... buffReader = new BufferedReader(new FileReader(inFile)); stBuilder = new StringBuilder(); line = null; while ((line = buffReader.readLine()) != null) { stBuilder.append(line); } buffReader.close(); XMLElement genesXML = new XMLElement(stBuilder.toString()); //freeing some memory I don't need anymore stBuilder.delete(0, stBuilder.length()); //reading file with the reference proteins set ArrayList<String> proteinsReferenceSet = new ArrayList<String>(); buffReader = new BufferedReader(new FileReader(fastaFile)); while ((line = buffReader.readLine()) != null) { if (line.charAt(0) == '>') { proteinsReferenceSet.add(line.split("\\|")[1]); } } buffReader.close(); Element pGenes = genesXML.asJDomElement().getChild(PredictedGenes.TAG_NAME); List<Element> contigs = pGenes.getChildren(ContigXML.TAG_NAME); System.out.println("There are " + contigs.size() + " contigs to be checked... "); outBuff.write("There are " + contigs.size() + " contigs to be checked... \n"); outBuff.write("Proteins reference set: \n"); for (String st : proteinsReferenceSet) { outBuff.write(st + ","); } outBuff.write("\n"); for (Element elem : contigs) { ContigXML contig = new ContigXML(elem); //escribo el id del contig en el que estoy outBuff.write("Checking contig: " + contig.getId() + "\n"); outBuff.flush(); List<XMLElement> geneList = contig.getChildrenWith(PredictedGene.TAG_NAME); System.out.println("geneList.size() = " + geneList.size()); int numeroDeGenesParaAnalizar = geneList.size() / FACTOR; if (numeroDeGenesParaAnalizar == 0) { numeroDeGenesParaAnalizar++; } ArrayList<Integer> indicesUtilizados = new ArrayList<Integer>(); outBuff.write("\nThe contig has " + geneList.size() + " predicted genes, let's analyze: " + numeroDeGenesParaAnalizar + "\n"); for (int j = 0; j < numeroDeGenesParaAnalizar; j++) { int geneIndex; boolean geneIsDismissed = false; do { geneIsDismissed = false; geneIndex = (int) Math.round(Math.floor(Math.random() * geneList.size())); PredictedGene tempGene = new PredictedGene(geneList.get(geneIndex).asJDomElement()); if (tempGene.getStatus().equals(PredictedGene.STATUS_DISMISSED)) { geneIsDismissed = true; } } while (indicesUtilizados.contains(new Integer(geneIndex)) && geneIsDismissed); indicesUtilizados.add(geneIndex); System.out.println("geneIndex = " + geneIndex); //Ahora hay que sacar el gen correspondiente al indice y hacer el control de calidad PredictedGene gene = new PredictedGene(geneList.get(geneIndex).asJDomElement()); outBuff.write("\nAnalyzing gene with id: " + gene.getId() + " , annotation uniprot id: " + gene.getAnnotationUniprotId() + "\n"); outBuff.write("eValue: " + gene.getEvalue() + "\n"); //--------------PETICION POST HTTP BLAST---------------------- PostMethod post = new PostMethod(BLAST_URL); post.addParameter("program", "blastx"); post.addParameter("sequence", gene.getSequence()); post.addParameter("database", "uniprotkb"); post.addParameter("email", "ppareja@era7.com"); post.addParameter("exp", "1e-10"); post.addParameter("stype", "dna"); // execute the POST HttpClient client = new HttpClient(); int status = client.executeMethod(post); System.out.println("status post = " + status); InputStream inStream = post.getResponseBodyAsStream(); String fileName = "jobid.txt"; FileOutputStream outStream = new FileOutputStream(new File(fileName)); byte[] buffer = new byte[1024]; int len; while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //Once the file is created I just have to read one line in order to extract the job id buffReader = new BufferedReader(new FileReader(new File(fileName))); String jobId = buffReader.readLine(); buffReader.close(); System.out.println("jobId = " + jobId); //--------------HTTP CHECK JOB STATUS REQUEST---------------------- GetMethod get = new GetMethod(CHECK_JOB_STATUS_URL + jobId); String jobStatus = ""; do { try { Thread.sleep(1000);//sleep for 1000 ms } catch (InterruptedException ie) { //If this thread was intrrupted by nother thread } status = client.executeMethod(get); //System.out.println("status get = " + status); inStream = get.getResponseBodyAsStream(); fileName = "jobStatus.txt"; outStream = new FileOutputStream(new File(fileName)); while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //Once the file is created I just have to read one line in order to extract the job id buffReader = new BufferedReader(new FileReader(new File(fileName))); jobStatus = buffReader.readLine(); //System.out.println("jobStatus = " + jobStatus); buffReader.close(); } while (!jobStatus.equals(FINISHED_JOB_STATUS)); //Once I'm here the blast should've already finished //--------------JOB RESULTS HTTP REQUEST---------------------- get = new GetMethod(JOB_RESULT_URL + jobId + "/out"); status = client.executeMethod(get); System.out.println("status get = " + status); inStream = get.getResponseBodyAsStream(); fileName = "jobResults.txt"; outStream = new FileOutputStream(new File(fileName)); while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //--------parsing the blast results file----- TreeSet<GeneEValuePair> featuresBlast = new TreeSet<GeneEValuePair>(); buffReader = new BufferedReader(new FileReader(new File(fileName))); while ((line = buffReader.readLine()) != null) { if (line.length() > 3) { String prefix = line.substring(0, 3); if (prefix.equals("TR:") || prefix.equals("SP:")) { String[] columns = line.split(" "); String id = columns[1]; //System.out.println("id = " + id); String e = ""; String[] arraySt = line.split("\\.\\.\\."); if (arraySt.length > 1) { arraySt = arraySt[1].trim().split(" "); int contador = 0; for (int k = 0; k < arraySt.length && contador <= 2; k++) { String string = arraySt[k]; if (!string.equals("")) { contador++; if (contador == 2) { e = string; } } } } else { //Number before e- String[] arr = arraySt[0].split("e-")[0].split(" "); String numeroAntesE = arr[arr.length - 1]; String numeroDespuesE = arraySt[0].split("e-")[1].split(" ")[0]; e = numeroAntesE + "e-" + numeroDespuesE; } double eValue = Double.parseDouble(e); //System.out.println("eValue = " + eValue); GeneEValuePair g = new GeneEValuePair(id, eValue); featuresBlast.add(g); } } } GeneEValuePair currentGeneEValuePair = new GeneEValuePair(gene.getAnnotationUniprotId(), gene.getEvalue()); System.out.println("currentGeneEValuePair.id = " + currentGeneEValuePair.id); System.out.println("currentGeneEValuePair.eValue = " + currentGeneEValuePair.eValue); boolean blastContainsGene = false; for (GeneEValuePair geneEValuePair : featuresBlast) { if (geneEValuePair.id.equals(currentGeneEValuePair.id)) { blastContainsGene = true; //le pongo la e que tiene en el wu-blast para poder comparar currentGeneEValuePair.eValue = geneEValuePair.eValue; break; } } if (blastContainsGene) { outBuff.write("The protein was found in the WU-BLAST result.. \n"); //Una vez que se que esta en el blast tengo que ver que sea la mejor GeneEValuePair first = featuresBlast.first(); outBuff.write("Protein with best eValue according to the WU-BLAST result: " + first.id + " , " + first.eValue + "\n"); if (first.id.equals(currentGeneEValuePair.id)) { outBuff.write("Proteins with best eValue match up \n"); } else { if (first.eValue == currentGeneEValuePair.eValue) { outBuff.write( "The one with best eValue is not the same protein but has the same eValue \n"); } else if (first.eValue > currentGeneEValuePair.eValue) { outBuff.write( "The one with best eValue is not the same protein but has a worse eValue :) \n"); } else { outBuff.write( "The best protein from BLAST has an eValue smaller than ours, checking if it's part of the reference set...\n"); //System.exit(-1); if (proteinsReferenceSet.contains(first.id)) { //The protein is in the reference set and that shouldn't happen outBuff.write( "The protein was found on the reference set, checking if it belongs to the same contig...\n"); String iterationSt = blastProteinsMap.get(gene.getAnnotationUniprotId()); if (iterationSt != null) { outBuff.write( "The protein was found in the BLAST used at the beginning of the annotation process.\n"); Iteration iteration = new Iteration(iterationSt); ArrayList<Hit> hits = iteration.getIterationHits(); boolean contigFound = false; Hit errorHit = null; for (Hit hit : hits) { if (hit.getHitDef().indexOf(contig.getId()) >= 0) { contigFound = true; errorHit = hit; break; } } if (contigFound) { outBuff.write( "ERROR: A hit from the same contig was find in the Blast file: \n" + errorHit.toString() + "\n"); } else { outBuff.write("There is no hit with the same contig! :)\n"); } } else { outBuff.write( "The protein is NOT in the BLAST used at the beginning of the annotation process.\n"); } } else { //The protein was not found on the reference set so everything's ok outBuff.write( "The protein was not found on the reference, everything's ok :)\n"); } } } } else { outBuff.write("The protein was NOT found on the WU-BLAST !! :( \n"); //System.exit(-1); } } } } catch (Exception ex) { ex.printStackTrace(); } finally { try { //closing outputfile outBuff.close(); } catch (IOException ex) { Logger.getLogger(AutomaticQualityControl.class.getName()).log(Level.SEVERE, null, ex); } } } }
From source file:de.mpg.imeji.presentation.util.UrlHelper.java
public static boolean isValidURI(URI uri) { try {/*w ww. j a v a 2s. c o m*/ HttpClient client = new HttpClient(); GetMethod method = new GetMethod(uri.toString()); client.executeMethod(method); return true; } catch (Exception e) { BeanHelper.error(((SessionBean) BeanHelper.getSessionBean(SessionBean.class)).getMessage("error") + " (Non valid URL): " + e); } return false; }
From source file:de.mpg.imeji.presentation.metadata.extractors.BasicExtractor.java
public static List<String> extractTechMd(Item item) throws Exception { List<String> techMd = new ArrayList<String>(); URI uri = item.getFullImageUrl(); String imageUrl = uri.toURL().toString(); GetMethod method = new GetMethod(imageUrl); method.setFollowRedirects(false);/*from w ww . j a va 2 s .co m*/ String userHandle = null; userHandle = LoginHelper.login(PropertyReader.getProperty("imeji.escidoc.user"), PropertyReader.getProperty("imeji.escidoc.password")); method.addRequestHeader("Cookie", "escidocCookie=" + userHandle); HttpClient client = new HttpClient(); client.executeMethod(method); InputStream input = method.getResponseBodyAsStream(); ImageInputStream iis = ImageIO.createImageInputStream(input); Iterator<ImageReader> readers = ImageIO.getImageReaders(iis); if (readers.hasNext()) { // pick the first available ImageReader ImageReader reader = readers.next(); // attach source to the reader reader.setInput(iis, true); // read metadata of first image IIOMetadata metadata = reader.getImageMetadata(0); String[] names = metadata.getMetadataFormatNames(); int length = names.length; for (int i = 0; i < length; i++) { displayMetadata(techMd, metadata.getAsTree(names[i])); } } return techMd; }
From source file:com.renlg.util.NetAssist.java
public static String delegateGet(String url) { StringBuffer response = new StringBuffer(); HttpClient client = new HttpClient(); HttpMethod method = null;/*from w w w . jav a 2 s .co m*/ try { method = new GetMethod(url); client.executeMethod(method); if (method.getStatusCode() == HttpStatus.SC_OK) { BufferedReader reader = new BufferedReader( new InputStreamReader(method.getResponseBodyAsStream(), "utf8")); String line; while ((line = reader.readLine()) != null) { response.append(line); } reader.close(); } } catch (Exception e) { log.error("HTTP Get" + url + "??", e); } finally { if (method != null) method.releaseConnection(); } return response.toString(); }
From source file:codeOrchestra.lcs.license.plimus.PlimusHelper.java
private static PlimusResponse executePlimusAction(String key, PlimusValidationAction action) throws IOException { GetMethod getMethod = new GetMethod(VALIDATION_URL); getMethod.getParams().setParameter("http.socket.timeout", new Integer(TIMEOUT)); getMethod.setQueryString(new NameValuePair[] { new NameValuePair("action", action.name()), new NameValuePair("productId", PRODUCT_ID), new NameValuePair("key", key) }); httpClient.executeMethod(getMethod); return new PlimusResponse(getMethod.getResponseBodyAsString()); }