Example usage for org.apache.commons.httpclient.methods PostMethod PostMethod

List of usage examples for org.apache.commons.httpclient.methods PostMethod PostMethod

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Introduction

In this page you can find the example usage for org.apache.commons.httpclient.methods PostMethod PostMethod.

Prototype

public PostMethod(String paramString)

Source Link

Usage

From source file:com.mycompany.jaxrsexample.client.Client.java

public static void main(String args[]) throws Exception {
    // Sent HTTP GET request to query all students info

    System.out.println("Invoking server through HTTP GET to query all students info");
    URL url = new URL("http://localhost:9000/studentservice/students");
    InputStream in = url.openStream();
    System.out.println(getStringFromInputStream(in));

    // Sent HTTP GET request to query student info
    System.out.println("Sent HTTP GET request to query customer info");
    url = new URL("http://localhost:9000/studentservice/students/1");
    in = url.openStream();// w  w w. jav a 2 s  . c o m
    System.out.println(getStringFromInputStream(in));

    // Sent HTTP PUT request to update student info
    System.out.println("\n");
    System.out.println("Sent HTTP PUT request to update student info");
    Client client = new Client();
    String inputFile = client.getClass().getResource("/update_student.xml").getFile();
    URIResolver resolver = new URIResolver(inputFile);
    File input = new File(resolver.getURI());
    PutMethod put = new PutMethod("http://localhost:9000/studentservice/students");
    RequestEntity entity = new FileRequestEntity(input, "text/xml; charset=ISO-8859-1");
    put.setRequestEntity(entity);
    HttpClient httpclient = new HttpClient();

    try {
        int result = httpclient.executeMethod(put);
        System.out.println("Response status code: " + result);
        System.out.println("Response body: ");
        System.out.println(put.getResponseBodyAsString());
    } finally {
        // Release current connection to the connection pool once you are
        // done
        put.releaseConnection();
    }

    // Sent HTTP POST request to add student
    System.out.println("\n");
    System.out.println("Sent HTTP POST request to add student");
    inputFile = client.getClass().getResource("/add_student.xml").getFile();
    resolver = new URIResolver(inputFile);
    input = new File(resolver.getURI());
    PostMethod post = new PostMethod("http://localhost:9000/studentservice/students");
    post.addRequestHeader("Accept", "text/xml");
    entity = new FileRequestEntity(input, "text/xml; charset=ISO-8859-1");
    post.setRequestEntity(entity);
    httpclient = new HttpClient();

    try {
        int result = httpclient.executeMethod(post);
        System.out.println("Response status code: " + result);
        System.out.println("Response body: ");
        System.out.println(post.getResponseBodyAsString());
    } finally {
        // Release current connection to the connection pool once you are
        // done
        post.releaseConnection();
    }

    System.out.println("\n");
    System.exit(0);
}

From source file:edu.techseekers.training.client.Client.java

public static void main(String args[]) throws Exception {
    // Sent HTTP GET request to query all customer info
    /*//from www  . j  a  v a  2  s .  c o m
     * URL url = new URL("http://localhost:9000/customers");
     * System.out.println("Invoking server through HTTP GET to query all
     * customer info"); InputStream in = url.openStream(); StreamSource
     * source = new StreamSource(in); printSource(source);
     */

    // Sent HTTP GET request to query customer info
    System.out.println("Sent HTTP GET request to query customer info");
    URL url = new URL("http://localhost:9000/customerservice/customers/123");
    InputStream in = url.openStream();
    System.out.println(getStringFromInputStream(in));

    // Sent HTTP GET request to query sub resource product info
    System.out.println("\n");
    System.out.println("Sent HTTP GET request to query sub resource product info");
    url = new URL("http://localhost:9000/customerservice/orders/223/products/323");
    in = url.openStream();
    System.out.println(getStringFromInputStream(in));

    // Sent HTTP PUT request to update customer info
    System.out.println("\n");
    System.out.println("Sent HTTP PUT request to update customer info");
    Client client = new Client();
    String inputFile = client.getClass().getResource("/update_customer.xml").getFile();
    URIResolver resolver = new URIResolver(inputFile);
    File input = new File(resolver.getURI());
    PutMethod put = new PutMethod("http://localhost:9000/customerservice/customers");
    RequestEntity entity = new FileRequestEntity(input, "text/xml; charset=ISO-8859-1");
    put.setRequestEntity(entity);
    HttpClient httpclient = new HttpClient();

    try {
        int result = httpclient.executeMethod(put);
        System.out.println("Response status code: " + result);
        System.out.println("Response body: ");
        System.out.println(put.getResponseBodyAsString());
    } finally {
        // Release current connection to the connection pool once you are
        // done
        put.releaseConnection();
    }

    // Sent HTTP POST request to add customer
    System.out.println("\n");
    System.out.println("Sent HTTP POST request to add customer");
    inputFile = client.getClass().getResource("/add_customer.xml").getFile();
    resolver = new URIResolver(inputFile);
    input = new File(resolver.getURI());
    PostMethod post = new PostMethod("http://localhost:9000/customerservice/customers");
    post.addRequestHeader("Accept", "text/xml");
    entity = new FileRequestEntity(input, "text/xml; charset=ISO-8859-1");
    post.setRequestEntity(entity);
    httpclient = new HttpClient();

    try {
        int result = httpclient.executeMethod(post);
        System.out.println("Response status code: " + result);
        System.out.println("Response body: ");
        System.out.println(post.getResponseBodyAsString());
    } finally {
        // Release current connection to the connection pool once you are
        // done
        post.releaseConnection();
    }

    System.out.println("\n");
    System.exit(0);
}

From source file:main.java.demo.jaxrs.client.Client.java

public static void main(String args[]) throws Exception {
    // Sent HTTP GET request to query all customer info
    /*//from w  w  w  .jav a 2 s. co m
     * URL url = new URL("http://localhost:9000/customers");
     * System.out.println("Invoking server through HTTP GET to query all
     * customer info"); InputStream in = url.openStream(); StreamSource
     * source = new StreamSource(in); printSource(source);
     */

    // Sent HTTP GET request to query customer info
    System.out.println("Sent HTTP GET request to query customer info");
    URL url = new URL("http://localhost:8989/RestFull/service1/customerservice/customers/123");
    InputStream in = url.openStream();
    System.out.println(getStringFromInputStream(in));

    // Sent HTTP GET request to query sub resource product info
    System.out.println("\n");
    System.out.println("Sent HTTP GET request to query sub resource product info");
    url = new URL("http://localhost:9000/customerservice/orders/223/products/323");
    in = url.openStream();
    System.out.println(getStringFromInputStream(in));

    // Sent HTTP PUT request to update customer info
    System.out.println("\n");
    System.out.println("Sent HTTP PUT request to update customer info");
    Client client = new Client();
    String inputFile = client.getClass().getResource("update_customer.xml").getFile();
    URIResolver resolver = new URIResolver(inputFile);
    File input = new File(resolver.getURI());
    PutMethod put = new PutMethod("http://localhost:9000/customerservice/customers");
    RequestEntity entity = new FileRequestEntity(input, "text/xml; charset=ISO-8859-1");
    put.setRequestEntity(entity);
    HttpClient httpclient = new HttpClient();

    try {
        int result = httpclient.executeMethod(put);
        System.out.println("Response status code: " + result);
        System.out.println("Response body: ");
        System.out.println(put.getResponseBodyAsString());
    } finally {
        // Release current connection to the connection pool once you are
        // done
        put.releaseConnection();
    }

    // Sent HTTP POST request to add customer
    System.out.println("\n");
    System.out.println("Sent HTTP POST request to add customer");
    inputFile = client.getClass().getResource("add_customer.xml").getFile();
    resolver = new URIResolver(inputFile);
    input = new File(resolver.getURI());
    PostMethod post = new PostMethod("http://localhost:9000/customerservice/customers");
    post.addRequestHeader("Accept", "text/xml");
    entity = new FileRequestEntity(input, "text/xml; charset=ISO-8859-1");
    post.setRequestEntity(entity);
    httpclient = new HttpClient();

    try {
        int result = httpclient.executeMethod(post);
        System.out.println("Response status code: " + result);
        System.out.println("Response body: ");
        System.out.println(post.getResponseBodyAsString());
    } finally {
        // Release current connection to the connection pool once you are
        // done
        post.releaseConnection();
    }

    System.out.println("\n");
    System.exit(0);
}

From source file:main.java.client.Client.java

public static void main(String args[]) throws Exception {
    // Sent HTTP GET request to query all customer info
    /*/*from   w ww.j av  a2 s  .  c  o  m*/
     * URL url = new URL("http://localhost:9000/customers");
     * System.out.println("Invoking server through HTTP GET to query all
     * customer info"); InputStream in = url.openStream(); StreamSource
     * source = new StreamSource(in); printSource(source);
     */

    // Sent HTTP GET request to query customer info
    System.out.println("Sent HTTP GET request to query customer info");
    URL url = new URL("http://localhost:8080/authenticate/customers/123");
    InputStream in = url.openStream();
    System.out.println(getStringFromInputStream(in));

    // Sent HTTP GET request to query sub resource product info
    System.out.println("\n");
    System.out.println("Sent HTTP GET request to query sub resource product info");
    url = new URL("http://localhost:9000/authenticate/orders/223/products/323");
    in = url.openStream();
    System.out.println(getStringFromInputStream(in));

    // Sent HTTP PUT request to update customer info
    System.out.println("\n");
    System.out.println("Sent HTTP PUT request to update customer info");
    Client client = new Client();
    String inputFile = client.getClass().getResource("/update_customer.xml").getFile();
    URIResolver resolver = new URIResolver(inputFile);
    File input = new File(resolver.getURI());
    PutMethod put = new PutMethod("http://localhost:9000/authenticate/customers");
    RequestEntity entity = new FileRequestEntity(input, "text/xml; charset=ISO-8859-1");
    put.setRequestEntity(entity);
    HttpClient httpclient = new HttpClient();

    try {
        int result = httpclient.executeMethod(put);
        System.out.println("Response status code: " + result);
        System.out.println("Response body: ");
        System.out.println(put.getResponseBodyAsString());
    } finally {
        // Release current connection to the connection pool once you are
        // done
        put.releaseConnection();
    }

    // Sent HTTP POST request to add customer
    System.out.println("\n");
    System.out.println("Sent HTTP POST request to add customer");
    inputFile = client.getClass().getResource("/add_customer.xml").getFile();
    resolver = new URIResolver(inputFile);
    input = new File(resolver.getURI());
    PostMethod post = new PostMethod("http://localhost:9000/authenticate/customers");
    post.addRequestHeader("Accept", "text/xml");
    entity = new FileRequestEntity(input, "text/xml; charset=ISO-8859-1");
    post.setRequestEntity(entity);
    httpclient = new HttpClient();

    try {
        int result = httpclient.executeMethod(post);
        System.out.println("Response status code: " + result);
        System.out.println("Response body: ");
        System.out.println(post.getResponseBodyAsString());
    } finally {
        // Release current connection to the connection pool once you are
        // done
        post.releaseConnection();
    }

    // Sent HTTP POST request to add json customer
    System.out.println("\n");
    System.out.println("Sent HTTP POST request to add json customer");
    String inputFilej = client.getClass().getResource("/add_customer.json").getFile();
    URIResolver resolverj = new URIResolver(inputFilej);
    File inputj = new File(resolverj.getURI());
    PostMethod postj = new PostMethod("http://localhost:9000/authenticate/customersjson");
    postj.addRequestHeader("Accept", "application/json");
    RequestEntity entityj = new FileRequestEntity(inputj, "application/json; charset=ISO-8859-1");
    postj.setRequestEntity(entityj);
    HttpClient httpclientj = new HttpClient();

    try {
        int resultj = httpclientj.executeMethod(postj);
        System.out.println("Response status code json: " + resultj);
        System.out.println("Response body json: ");
        System.out.println(postj.getResponseBodyAsString());
    } finally {
        // Release current connection to the connection pool once you are
        // done
        postj.releaseConnection();
    }
    System.out.println("\n");
    System.exit(0);
}

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  w  w  .j  av a2 s  . c o  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: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  .c om

        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:dk.statsbiblioteket.doms.licensemodule.integrationtest.HttpClientPoster.java

public static String postJSON(String url, String content) throws Exception {

    HttpClient client = new HttpClient();
    client.getParams().setParameter("http.useragent", "Dokumentleveringweb XML client");

    BufferedReader br = null;/*from   w  ww.j  ava 2  s  .  c  o  m*/

    //TODO property
    PostMethod method = new PostMethod(url);

    method.addRequestHeader("Content-Type", "application/json;charset=UTF-8");
    method.setRequestBody(content); // How to do this a non-deprecated way?

    try {
        int httpCode = client.executeMethod(method);
        br = new BufferedReader(new InputStreamReader(method.getResponseBodyAsStream()));

        String readLine;
        StringBuilder response = new StringBuilder();
        while (((readLine = br.readLine()) != null)) {
            response.append(readLine);

        }
        return response.toString();

    } catch (Exception e) {
        throw e;
    } finally {
        method.releaseConnection();
        if (br != null)
            try {
                br.close();
            } catch (Exception fe) {
                fe.printStackTrace();
            }
    }

}

From source file:com.leosys.core.utils.SendMessage.java

public static String postMessage(String phoneNo, String sendText) throws IOException {
    HttpClient client = new HttpClient();
    PostMethod post = new PostMethod("http://sms.webchinese.cn/web_api/");
    post.addRequestHeader("Content-Type", "application/x-www-form-urlencoded;charset=gbk");// ?    
    NameValuePair[] data = { new NameValuePair("Uid", "fanyy"), // ??    
            new NameValuePair("Key", "694de3e5ca9f7015eaef"), // ??,    
            new NameValuePair("smsMob", phoneNo), // ??    
            new NameValuePair("smsText", sendText + "??") };//  
    post.setRequestBody(data);/*w  w w .j a v a2  s.co  m*/

    client.executeMethod(post);
    Header[] headers = post.getResponseHeaders();
    int statusCode = post.getStatusCode();
    System.out.println("statusCode:" + statusCode);
    for (Header h : headers) {
        System.out.println(h.toString());
    }
    String result = new String(post.getResponseBodyAsString().getBytes("gbk"));
    System.out.println(result);
    post.releaseConnection();
    return result;
}

From source file:com.oneapm.base.tools.UrlPostMethod.java

public static void urlPostMethod(String url, String json) {

    HttpClient httpClient = new HttpClient();
    PostMethod method = new PostMethod(url);
    try {/* ww w .j av  a  2  s  . c  o m*/
        if (json != null && !json.trim().equals("")) {
            RequestEntity requestEntity = new StringRequestEntity(json, "application/x-www-form-urlencoded",
                    "utf-8");
            method.setRequestEntity(requestEntity);
        }
        long startTime = System.currentTimeMillis();
        int x = httpClient.executeMethod(method);
        long elapsedTime = System.currentTimeMillis();

        System.out.println(x + ":" + (elapsedTime - startTime));

    } catch (IOException e) {
        e.printStackTrace();
    } finally {
        method.releaseConnection();
    }
}

From source file:com.pieframework.runtime.utils.CampfireNotifier.java

public static boolean notify(String msg, String url, String user, String password) {
    HttpClient client = new HttpClient();
    PostMethod post = new PostMethod(url);

    // stuff the Authorization request header
    byte[] encodedPassword = (user + ":" + password).getBytes();
    BASE64Encoder encoder = new BASE64Encoder();
    post.setRequestHeader("Authorization", "Basic " + encoder.encode(encodedPassword));

    try {/*  w  w w .j  av a2  s.c  o  m*/
        RequestEntity entity = new StringRequestEntity("<message><body>" + msg + "</body></message>",
                "application/xml", "UTF-8");
        post.setRequestEntity(entity);
        client.executeMethod(post);
        String responseMsg = "httpStatus: " + post.getStatusCode() + " " + "Content-type: "
                + post.getResponseHeader("Content-Type") + " " + post.getResponseBodyAsString();
        Configuration.log().info(responseMsg);
    } catch (Exception e) {
        e.printStackTrace();
    }

    return true;
}