Example usage for org.apache.http.client HttpClient getParams

List of usage examples for org.apache.http.client HttpClient getParams

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Introduction

In this page you can find the example usage for org.apache.http.client HttpClient getParams.

Prototype

@Deprecated
HttpParams getParams();

Source Link

Document

Obtains the parameters for this client.

Usage

From source file:org.fedoraproject.eclipse.packager.api.UploadSourceCommand.java

/**
 * Wrap a basic HttpClient object in a Fedora SSL enabled HttpClient (which includes
 * Fedora SSL authentication cert) object.
 * // w  ww .j  a v  a  2s .  c om
 * @param base The HttpClient to wrap.
 * @return The SSL wrapped HttpClient.
 * @throws GeneralSecurityException
 * @throws IOException
 */
private HttpClient fedoraSslEnable(HttpClient base)
        throws GeneralSecurityException, FileNotFoundException, IOException {

    // Get a SSL related instance for setting up SSL connections.
    FedoraSSL fedoraSSL = FedoraSSLFactory.getInstance();
    SSLSocketFactory sf = new SSLSocketFactory(fedoraSSL.getInitializedSSLContext(), // may throw FileNotFoundE
            SSLSocketFactory.ALLOW_ALL_HOSTNAME_VERIFIER);
    ClientConnectionManager ccm = base.getConnectionManager();
    SchemeRegistry sr = ccm.getSchemeRegistry();
    Scheme https = new Scheme("https", 443, sf); //$NON-NLS-1$
    sr.register(https);
    return new DefaultHttpClient(ccm, base.getParams());
}

From source file:com.strato.hidrive.api.connection.httpgateway.HTTPGateway.java

/**
 * wrap an httpclient with this stub for prevent ssl unverified exceptions (for testing purposes) 
 *///from   ww w.  j av a2s.  c  om
public DefaultHttpClient sslStubClient(HttpClient client) {
    try {
        X509TrustManager tm = new X509TrustManager() {
            public void checkClientTrusted(X509Certificate[] xcs, String string) throws CertificateException {
            }

            public void checkServerTrusted(X509Certificate[] xcs, String string) throws CertificateException {
            }

            public X509Certificate[] getAcceptedIssuers() {
                return null;
            }
        };
        SSLContext ctx = SSLContext.getInstance("TLS");
        ctx.init(null, new TrustManager[] { tm }, null);
        SSLSocketFactory ssf = new StubSSLSocketFactory(ctx);
        ssf.setHostnameVerifier(SSLSocketFactory.ALLOW_ALL_HOSTNAME_VERIFIER);
        ClientConnectionManager ccm = client.getConnectionManager();
        SchemeRegistry sr = ccm.getSchemeRegistry();
        sr.register(new Scheme("https", ssf, 443));
        return new DefaultHttpClient(ccm, client.getParams());
    } catch (Exception ex) {
        return null;
    }
}

From source file:duthientan.mmanm.com.Main.java

private void jButton1ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButton1ActionPerformed
    // TODO add your handling code here:
    try {/*w  ww  . j a  va  2s  . c  om*/
        HttpClient httpclient = new DefaultHttpClient();
        httpclient.getParams().setParameter(CoreProtocolPNames.PROTOCOL_VERSION, HttpVersion.HTTP_1_1);
        HttpGet httpGet = new HttpGet("http://localhost:4000/api/store");
        httpGet.setHeader("id", id);
        httpGet.addHeader("x-access-token", token);
        HttpResponse response = httpclient.execute(httpGet);
        JSONObject obj = new JSONObject(EntityUtils.toString(response.getEntity()));
        //System.out.println(EntityUtils.toString(response.getEntity()));
        JSONArray jsonArr = obj.getJSONArray("arr");
        String result = "";
        for (int i = 0; i < jsonArr.length(); i++) {
            result += "http://localhost:4000/" + jsonArr.get(i).toString() + "\n";
        }
        textLinkFile.setText(result);
    } catch (IOException ex) {
        Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
    }
}

From source file:duthientan.mmanm.com.Main.java

private void btnUploadFileActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_btnUploadFileActionPerformed
    // TODO add your handling code here:
    if (!fileUploadPath.equals("")) {
        progressBarCipher.setIndeterminate(true);
        new Thread(new Runnable() {
            @Override/*ww  w .  j  a  v  a 2s  .  c  om*/
            public void run() {
                try {
                    HttpClient httpclient = new DefaultHttpClient();
                    httpclient.getParams().setParameter(CoreProtocolPNames.PROTOCOL_VERSION,
                            HttpVersion.HTTP_1_1);
                    HttpPost httppost = new HttpPost("http://localhost:4000/api/upload");
                    File file = new File(fileUploadPath);
                    MultipartEntity mpEntity = new MultipartEntity();
                    ContentBody cbFile = new FileBody(file);
                    mpEntity.addPart("files", cbFile);
                    httppost.addHeader("id", id);
                    httppost.addHeader("x-access-token", token);
                    httppost.setEntity(mpEntity);
                    HttpResponse response = httpclient.execute(httppost);
                    HttpEntity resEntity = response.getEntity();
                    progressBarCipher.setIndeterminate(false);
                    JFrame frame = new JFrame("Upload Completed");
                    JOptionPane.showMessageDialog(frame, "File Uploaded");
                } catch (IOException ex) {
                    Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
                }
            }
        }).start();
    } else {
        JFrame frame = new JFrame("File not Found");
        JOptionPane.showMessageDialog(frame, "Plase Choice File Upload");
    }
}

From source file:org.jvoicexml.documentserver.schemestrategy.HttpSchemeStrategy.java

/**
 * {@inheritDoc}/*  ww  w.j  a v a  2 s  . c  o  m*/
 */
@Override
public InputStream getInputStream(final String sessionId, final URI uri, final RequestMethod method,
        final long timeout, final Collection<KeyValuePair> parameters) throws BadFetchError {
    final HttpClient client = SESSION_STORAGE.getSessionIdentifier(sessionId);
    final URI fullUri;
    try {
        final URI fragmentLessUri = new URI(uri.getScheme(), uri.getAuthority(), uri.getPath(), uri.getQuery(),
                null);
        fullUri = addParameters(parameters, fragmentLessUri);
    } catch (URISyntaxException e) {
        throw new BadFetchError(e.getMessage(), e);
    } catch (SemanticError e) {
        throw new BadFetchError(e.getMessage(), e);
    }
    final String url = fullUri.toString();
    if (LOGGER.isDebugEnabled()) {
        LOGGER.debug("connecting to '" + url + "'...");
    }

    final HttpUriRequest request;
    if (method == RequestMethod.GET) {
        request = new HttpGet(url);
    } else {
        request = new HttpPost(url);
    }
    attachFiles(request, parameters);
    try {
        final HttpParams params = client.getParams();
        setTimeout(timeout, params);
        final HttpResponse response = client.execute(request);
        final StatusLine statusLine = response.getStatusLine();
        final int status = statusLine.getStatusCode();
        if (status != HttpStatus.SC_OK) {
            throw new BadFetchError(statusLine.getReasonPhrase() + " (HTTP error code " + status + ")");
        }
        final HttpEntity entity = response.getEntity();
        return entity.getContent();
    } catch (IOException e) {
        throw new BadFetchError(e.getMessage(), e);
    }
}

From source file:it.iit.genomics.cru.structures.bridges.uniprot.UniprotkbUtils.java

private Collection<MoleculeEntry> getUniprotEntriesXML(String location, boolean waitAndRetryOnFailure)
        throws BridgesRemoteAccessException {

    String url = location + "&format=xml";

    ArrayList<MoleculeEntry> uniprotEntries = new ArrayList<>();
    try {//from   ww w .  j  a v a  2s . co m
        HttpClient client = new DefaultHttpClient();
        client.getParams().setParameter(ClientPNames.ALLOW_CIRCULAR_REDIRECTS, Boolean.TRUE);
        HttpGet request = new HttpGet(url);

        // add request header
        request.addHeader("User-Agent", USER_AGENT);

        HttpResponse response = client.execute(request);

        if (response.getEntity().getContentLength() == 0) {
            // No result
            return uniprotEntries;
        }

        DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
        DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
        Document doc = dBuilder.parse(new InputSource(response.getEntity().getContent()));

        // optional, but recommended
        // read this -
        // http://stackoverflow.com/questions/13786607/normalization-in-dom-parsing-with-java-how-does-it-work
        doc.getDocumentElement().normalize();

        // interaction structure
        NodeList entryList = doc.getElementsByTagName("entry");

        for (int i = 0; i < entryList.getLength(); i++) {

            Element entryElement = (Element) entryList.item(i);

            String dataset = entryElement.getAttribute("dataset");

            String ac = entryElement.getElementsByTagName("accession").item(0).getFirstChild().getNodeValue();

            MoleculeEntry uniprotEntry = new MoleculeEntry(ac);

            uniprotEntry.setDataset(dataset);

            // Taxid
            Element organism = (Element) entryElement.getElementsByTagName("organism").item(0);

            String organismCommonName = null;
            String organismScientificName = null;
            String organismOtherName = null;

            NodeList organismNames = organism.getElementsByTagName("name");

            for (int j = 0; j < organismNames.getLength(); j++) {

                Element reference = (Element) organismNames.item(j);
                switch (reference.getAttribute("type")) {
                case "scientific":
                    organismScientificName = reference.getTextContent();
                    break;
                case "common":
                    organismCommonName = reference.getTextContent();
                    break;
                default:
                    organismOtherName = reference.getTextContent();
                    break;
                }
            }

            if (null != organismCommonName) {
                uniprotEntry.setOrganism(organismCommonName);
            } else if (null != organismScientificName) {
                uniprotEntry.setOrganism(organismScientificName);
            } else if (null != organismOtherName) {
                uniprotEntry.setOrganism(organismOtherName);
            }

            NodeList organismReferences = organism.getElementsByTagName("dbReference");

            for (int j = 0; j < organismReferences.getLength(); j++) {
                Element reference = (Element) organismReferences.item(j);
                if (reference.hasAttribute("type") && "NCBI Taxonomy".equals(reference.getAttribute("type"))) {
                    String proteinTaxid = reference.getAttribute("id");
                    uniprotEntry.setTaxid(proteinTaxid);
                }
            }

            // GENE
            NodeList geneNames = entryElement.getElementsByTagName("gene");

            for (int j = 0; j < geneNames.getLength(); j++) {
                Element gene = (Element) geneNames.item(j);

                NodeList nameList = gene.getElementsByTagName("name");

                for (int k = 0; k < nameList.getLength(); k++) {
                    Element name = (Element) nameList.item(k);
                    uniprotEntry.addGeneName(name.getFirstChild().getNodeValue());
                }
            }

            // modified residues
            HashMap<String, ModifiedResidue> modifiedResidues = new HashMap<>();

            NodeList features = entryElement.getElementsByTagName("feature");
            for (int j = 0; j < features.getLength(); j++) {
                Element feature = (Element) features.item(j);

                if (false == entryElement.equals(feature.getParentNode())) {
                    continue;
                }

                // ensembl
                if (feature.hasAttribute("type") && "modified residue".equals(feature.getAttribute("type"))) {

                    String description = feature.getAttribute("description").split(";")[0];

                    if (false == modifiedResidues.containsKey(description)) {
                        modifiedResidues.put(description, new ModifiedResidue(description));
                    }

                    NodeList locations = feature.getElementsByTagName("location");
                    for (int k = 0; k < locations.getLength(); k++) {
                        Element loc = (Element) locations.item(k);
                        NodeList positions = loc.getElementsByTagName("position");
                        for (int l = 0; l < positions.getLength(); l++) {
                            Element position = (Element) positions.item(l);
                            modifiedResidues.get(description).addPosition(
                                    new UniprotPosition(Integer.parseInt(position.getAttribute("position"))));
                        }

                    }
                }
            }

            uniprotEntry.getModifications().addAll(modifiedResidues.values());

            // Xrefs:
            NodeList dbReferences = entryElement.getElementsByTagName("dbReference");
            for (int j = 0; j < dbReferences.getLength(); j++) {
                Element dbReference = (Element) dbReferences.item(j);

                if (false == entryElement.equals(dbReference.getParentNode())) {
                    continue;
                }

                NodeList molecules = dbReference.getElementsByTagName("molecule");

                // ensembl
                if (dbReference.hasAttribute("type") && "Ensembl".equals(dbReference.getAttribute("type"))) {

                    // transcript ID
                    String id = dbReference.getAttribute("id");

                    for (int iMolecule = 0; iMolecule < molecules.getLength(); iMolecule++) {
                        Element molecule = (Element) molecules.item(iMolecule);
                        uniprotEntry.addXrefToVarSplice(id, molecule.getAttribute("id"));
                    }

                    uniprotEntry.addEnsemblGene(id);

                    NodeList properties = dbReference.getElementsByTagName("property");

                    for (int k = 0; k < properties.getLength(); k++) {
                        Element property = (Element) properties.item(k);

                        if (property.hasAttribute("type") && "gene ID".equals(property.getAttribute("type"))) {
                            uniprotEntry.addEnsemblGene(property.getAttribute("value"));
                        }
                    }
                }

                // refseq
                if (dbReference.hasAttribute("type") && "RefSeq".equals(dbReference.getAttribute("type"))) {
                    NodeList properties = dbReference.getElementsByTagName("property");
                    for (int k = 0; k < properties.getLength(); k++) {
                        Element property = (Element) properties.item(k);
                        if (property.hasAttribute("type")
                                && "nucleotide sequence ID".equals(property.getAttribute("type"))) {

                            String id = property.getAttribute("value");
                            if (molecules.getLength() > 0) {
                                for (int iMolecule = 0; iMolecule < molecules.getLength(); iMolecule++) {
                                    Element molecule = (Element) molecules.item(iMolecule);

                                    // If refseq, add also without the version                                       
                                    uniprotEntry.addXrefToVarSplice(id, molecule.getAttribute("id"));
                                    uniprotEntry.addXrefToVarSplice(id.split("\\.")[0],
                                            molecule.getAttribute("id"));

                                }
                            } else {
                                // If refseq, add also without the version                                       
                                uniprotEntry.addXrefToVarSplice(id, ac);
                                uniprotEntry.addXrefToVarSplice(id.split("\\.")[0], ac);
                            }

                            uniprotEntry.addRefseq(id);

                        }
                    }
                }

                /* PDB chains will be imported from the webservice */
                // PDB
                if (dbReference.hasAttribute("type") && "PDB".equals(dbReference.getAttribute("type"))) {
                    NodeList properties = dbReference.getElementsByTagName("property");
                    String method = null;
                    String chains = null;

                    for (int k = 0; k < properties.getLength(); k++) {
                        Element property = (Element) properties.item(k);
                        if (property.hasAttribute("type") && "method".equals(property.getAttribute("type"))) {
                            method = property.getAttribute("value");
                        } else if (property.hasAttribute("type")
                                && "chains".equals(property.getAttribute("type"))) {
                            chains = property.getAttribute("value");
                        }
                    }

                    if (method != null && "Model".equals(method)) {
                        continue;
                    }

                    if (chains == null) {
                        continue;
                    }

                    String pdb = dbReference.getAttribute("id");

                    uniprotEntry.addPDB(pdb, method);

                    for (String chainElement : chains.split(",")) {
                        try {
                            String chainNames = chainElement.split("=")[0];
                            int start = Integer.parseInt(chainElement.split("=")[1].trim().split("-")[0]);
                            int end = Integer
                                    .parseInt(chainElement.split("=")[1].trim().split("-")[1].replace(".", ""));
                            for (String chainName : chainNames.split("/")) {
                                uniprotEntry.addChain(pdb, new ChainMapping(pdb, chainName.trim(), start, end),
                                        method);
                            }
                        } catch (ArrayIndexOutOfBoundsException aiobe) {
                            // IGBLogger.getInstance().warning(
                            // "Cannot parse chain: " + chainElement
                            // + ", skip");
                        }
                    }
                }

            }

            // Sequence
            NodeList sequenceElements = entryElement.getElementsByTagName("sequence");

            for (int j = 0; j < sequenceElements.getLength(); j++) {
                Element sequenceElement = (Element) sequenceElements.item(j);

                if (false == sequenceElement.getParentNode().equals(entryElement)) {
                    continue;
                }
                String sequence = sequenceElement.getFirstChild().getNodeValue().replaceAll("\n", "");
                uniprotEntry.setSequence(sequence);
            }

            // Diseases
            NodeList diseases = entryElement.getElementsByTagName("disease");

            for (int j = 0; j < diseases.getLength(); j++) {
                Element disease = (Element) diseases.item(j);

                NodeList nameList = disease.getElementsByTagName("name");

                for (int k = 0; k < nameList.getLength(); k++) {
                    Element name = (Element) nameList.item(k);
                    uniprotEntry.addDisease(name.getFirstChild().getNodeValue());
                }
            }

            // Get fasta for all varsplice
            String fastaQuery = "http://www.uniprot.org/uniprot/" + uniprotEntry.getUniprotAc()
                    + ".fasta?include=yes";

            try {
                //HttpClient fastaClient = new DefaultHttpClient();

                client.getParams().setParameter(ClientPNames.ALLOW_CIRCULAR_REDIRECTS, Boolean.TRUE);
                HttpGet fastaRequest = new HttpGet(fastaQuery);

                // add request header
                request.addHeader("User-Agent", USER_AGENT);

                HttpResponse fastaResponse = client.execute(fastaRequest);

                if (fastaResponse.getEntity().getContentLength() == 0) {
                    continue;
                }

                InputStream is = fastaResponse.getEntity().getContent();

                try {
                    LinkedHashMap<String, ProteinSequence> fasta = FastaReaderHelper
                            .readFastaProteinSequence(is);

                    boolean mainSequence = true;

                    for (ProteinSequence seq : fasta.values()) {
                        //                            logger.info("Add sequence: " + seq.getAccession().getID() + " : " + seq.getSequenceAsString());
                        uniprotEntry.addSequence(seq.getAccession().getID(), seq.getSequenceAsString());
                        if (mainSequence) {
                            uniprotEntry.setMainIsoform(seq.getAccession().getID());
                            mainSequence = false;
                        }
                    }
                } catch (Exception e) {
                    logger.error("Cannot retrieve fasta for : " + uniprotEntry.getUniprotAc());
                }
            } catch (IOException | IllegalStateException ex) {
                logger.error(null, ex);
            }

            uniprotEntries.add(uniprotEntry);

        }

    } catch (SAXParseException se) {
        // Nothing was return
        // IGBLogger.getInstance()
        // .error("Uniprot returns empty result: " + url);
    } catch (IOException | ParserConfigurationException | IllegalStateException | SAXException | DOMException
            | NumberFormatException e) {
        if (waitAndRetryOnFailure && allowedUniprotFailures > 0) {
            try {
                allowedUniprotFailures--;
                Thread.sleep(5000);
                return getUniprotEntriesXML(location, false);
            } catch (InterruptedException e1) {
                logger.error("Fail to retrieve data from " + location);
                throw new BridgesRemoteAccessException("Fail to retrieve data from Uniprot " + location);
            }
        } else {
            logger.error("Problem with Uniprot: " + url);
            throw new BridgesRemoteAccessException("Fail to retrieve data from Uniprot " + location);
        }
    }

    for (MoleculeEntry entry : uniprotEntries) {
        addToCache(entry);
    }

    return uniprotEntries;
}

From source file:org.cgiar.ccafs.ap.util.ClientRepository.java

public DefaultHttpClient verifiedClient(HttpClient base) {
    try {//from ww w  .  j a  v  a2 s . c  o  m
        SSLContext ctx = SSLContext.getInstance("SSL");
        X509TrustManager tm = new X509TrustManager() {

            @Override
            public void checkClientTrusted(X509Certificate[] chain, String authType)
                    throws CertificateException {
            }

            @Override
            public void checkServerTrusted(X509Certificate[] chain, String authType)
                    throws CertificateException {
            }

            @Override
            public java.security.cert.X509Certificate[] getAcceptedIssuers() {
                return null;
            }
        };

        ctx.init(null, new TrustManager[] { tm }, null);
        SSLSocketFactory ssf = new SSLSocketFactory(ctx, SSLSocketFactory.ALLOW_ALL_HOSTNAME_VERIFIER);
        ClientConnectionManager mgr = base.getConnectionManager();
        SchemeRegistry registry = mgr.getSchemeRegistry();
        registry.register(new Scheme("https", 443, ssf));
        return new DefaultHttpClient(mgr, base.getParams());
    } catch (Exception ex) {
        ex.printStackTrace();
        return null;
    }
}

From source file:uk.ac.brighton.ci360.bigarrow.PlacesAPISearch.java

@SuppressWarnings("unused")
private HttpClient sslClient(HttpClient client) {
    try {//  w w  w .j ava 2s .  c om
        X509TrustManager tm = new X509TrustManager() {
            public void checkClientTrusted(X509Certificate[] xcs, String string) throws CertificateException {
            }

            public void checkServerTrusted(X509Certificate[] xcs, String string) throws CertificateException {
            }

            public X509Certificate[] getAcceptedIssuers() {
                return null;
            }
        };
        SSLContext ctx = SSLContext.getInstance("TLS");
        ctx.init(null, new TrustManager[] { tm }, null);
        SSLSocketFactory ssf = new MySSLSocketFactory(ctx);
        ssf.setHostnameVerifier(SSLSocketFactory.ALLOW_ALL_HOSTNAME_VERIFIER);
        ClientConnectionManager ccm = client.getConnectionManager();
        SchemeRegistry sr = ccm.getSchemeRegistry();
        sr.register(new Scheme("https", ssf, 443));
        return new DefaultHttpClient(ccm, client.getParams());
    } catch (Exception ex) {
        return null;
    }
}