/*
 * Copyright (c) 2007-2012 The Broad Institute, Inc.
 * SOFTWARE COPYRIGHT NOTICE
 * This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
 *
 * This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
 *
 * This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
 * Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
 */

package org.broad.igv.util;

import biz.source_code.base64Coder.Base64Coder;
import net.sf.samtools.seekablestream.SeekableStream;
import net.sf.samtools.util.ftp.FTPClient;
import net.sf.samtools.util.ftp.FTPStream;
import net.sf.samtools.util.ftp.FTPUtils;
import org.apache.log4j.Logger;
import org.apache.tomcat.util.HttpDate;
import org.broad.igv.Globals;
import org.broad.igv.PreferenceManager;
import org.broad.igv.exceptions.HttpResponseException;
import org.broad.igv.gs.GSUtils;
import org.broad.igv.ui.IGV;
import org.broad.igv.util.stream.IGVSeekableHTTPStream;
import org.broad.igv.util.stream.IGVUrlHelper;

import javax.net.ssl.HttpsURLConnection;
import javax.net.ssl.SSLContext;
import javax.net.ssl.TrustManager;
import javax.net.ssl.X509TrustManager;
import java.awt.*;
import java.io.*;
import java.net.*;
import java.security.KeyManagementException;
import java.security.NoSuchAlgorithmException;
import java.util.*;
import java.util.List;
import java.util.regex.Pattern;
import java.util.zip.GZIPInputStream;

/**
 * Wrapper utility class... for interacting with HttpURLConnection.
 *
 * @author Jim Robinson
 * @date 9/22/11
 */
public class HttpUtils {

    private static Logger log = Logger.getLogger(HttpUtils.class);

    private static HttpUtils instance;

    private Map<String, Boolean> byteRangeTestMap;

    private ProxySettings proxySettings = null;
    private final int MAX_REDIRECTS = 5;

    private String defaultUserName = null;
    private char[] defaultPassword = null;
    private static Pattern URLmatcher = Pattern.compile(".{1,8}://.*");

    // static provided to support unit testing
    private static boolean BYTE_RANGE_DISABLED = false;

    /**
     * @return the single instance
     */
    public static HttpUtils getInstance() {
        if (instance == null) {
            instance = new HttpUtils();
        }
        return instance;
    }

    private HttpUtils() {

        org.broad.tribble.util.ParsingUtils.registerHelperClass(IGVUrlHelper.class);

        disableCertificateValidation();
        CookieHandler.setDefault(new IGVCookieManager());
        Authenticator.setDefault(new IGVAuthenticator());

        byteRangeTestMap = Collections.synchronizedMap(new HashMap());
    }

    public static boolean isRemoteURL(String string) {
        String lcString = string.toLowerCase();
        return lcString.startsWith("http://") || lcString.startsWith("https://") || lcString.startsWith("ftp://");
    }

    /**
     * Provided to support unit testing (force disable byte range requests)
     *
     * @return
     */
    public static void disableByteRange(boolean b) {
        BYTE_RANGE_DISABLED = b;
    }


    /**
     * @param elements
     * @param joiner
     * @return
     * @deprecated HttpUtils.openConnection does URL encoding itself
     *             <p/>
     *             Join the {@code elements} with the character {@code joiner},
     *             URLencoding the {@code elements} along the way. {@code joiner}
     *             is NOT URLEncoded
     *             Example:
     *             String[] parm_list = new String[]{"app les", "oranges", "bananas"};
     *             String formatted = buildURLString(Arrays.asList(parm_list), "+");
     *             <p/>
     *             formatted will be "app%20les+oranges+bananas"
     */
    @Deprecated
    public static String buildURLString(Iterable<String> elements, String joiner) {

        Iterator<String> iter = elements.iterator();
        if (!iter.hasNext()) {
            return "";
        }
        String wholequery = iter.next();
        try {
            while (iter.hasNext()) {
                wholequery += joiner + URLEncoder.encode(iter.next(), "UTF-8");
            }
            return wholequery;
        } catch (UnsupportedEncodingException e) {
            throw new IllegalArgumentException("Bad argument in genelist: " + e.getMessage());
        }
    }


    /**
     * Return the contents of the url as a String.  This method should only be used for queries expected to return
     * a small amount of data.
     *
     * @param url
     * @return
     * @throws IOException
     */
    public String getContentsAsString(URL url) throws IOException {

        InputStream is = null;
        HttpURLConnection conn = openConnection(url, null);
        try {
            is = conn.getInputStream();
            return readContents(is);

        } finally {
            if (is != null) is.close();
        }
    }

    public String getContentsAsJSON(URL url) throws IOException {

        InputStream is = null;
        Map<String, String> reqProperties = new HashMap();
        reqProperties.put("Accept", "application/json,text/plain");
        HttpURLConnection conn = openConnection(url, reqProperties);
        try {
            is = conn.getInputStream();
            return readContents(is);

        } finally {
            if (is != null) is.close();
        }
    }

    /**
     * Open a connection stream for the URL.
     *
     * @param url
     * @return
     * @throws IOException
     */
    public InputStream openConnectionStream(URL url) throws IOException {
        log.debug("Opening connection stream to  " + url);
        if (url.getProtocol().toLowerCase().equals("ftp")) {
            String userInfo = url.getUserInfo();
            String host = url.getHost();
            String file = url.getPath();
            FTPClient ftp = FTPUtils.connect(host, userInfo, new UserPasswordInputImpl());
            ftp.pasv();
            ftp.retr(file);
            return new FTPStream(ftp);

        } else {
            return openConnectionStream(url, null);
        }
    }

    public InputStream openConnectionStream(URL url, Map<String, String> requestProperties) throws IOException {

        HttpURLConnection conn = openConnection(url, requestProperties);
        if (conn == null)
            return null;
        InputStream input = conn.getInputStream();
        if ("gzip".equals(conn.getContentEncoding())) {
            input = new GZIPInputStream(input);
        }
        return input;
    }


    public boolean resourceAvailable(URL url) {
        log.debug("Checking if resource is available: " + url);
        if (url.getProtocol().toLowerCase().equals("ftp")) {
            return FTPUtils.resourceAvailable(url);
        }

        try {
            HttpURLConnection conn = openConnection(url, null, "HEAD");
            int code = conn.getResponseCode();
            return code == 200;
        } catch (IOException e) {
            return false;
        }
    }

    public String getHeaderField(URL url, String key) throws IOException {
        HttpURLConnection conn = openConnection(url, null, "HEAD");
        if (conn == null) return null;
        return conn.getHeaderField(key);
    }

    public long getLastModified(URL url) throws IOException {
        HttpURLConnection conn = openConnection(url, null, "HEAD");
        if (conn == null) return 0;
        return conn.getLastModified();
    }

    public long getContentLength(URL url) throws IOException {

        String contentLengthString = getHeaderField(url, "Content-Length");
        if (contentLengthString == null) {
            return -1;
        } else {
            return Long.parseLong(contentLengthString);
        }
    }

    /**
     * Compare a local and remote resource.
     *
     * @param file
     * @param url
     * @return true if the files are "the same", false if the remote file has been modified wrt the local one.
     * @throws IOException
     */
    public boolean compareResources(File file, URL url) throws IOException {


        if (!file.exists()) {
            return false;
        }

        HttpURLConnection conn = openConnection(url, null, "HEAD");

        // Check content-length first
        long contentLength = -1;
        String contentLengthString = conn.getHeaderField("Content-Length");
        if (contentLengthString != null) {
            try {
                contentLength = Long.parseLong(contentLengthString);
            } catch (NumberFormatException e) {
                log.error("Error parsing content-length string: " + contentLengthString + " from URL: "
                        + url.toString());
                contentLength = -1;
            }
        }
        if (contentLength != file.length()) {
            return false;
        }

        // Compare last-modified dates
        String lastModifiedString = conn.getHeaderField("Last-Modified");
        if (lastModifiedString == null) {
            return false;
        } else {
            HttpDate date = new HttpDate();
            date.parse(lastModifiedString);
            long remoteModifiedTime = date.getTime();
            long localModifiedTime = file.lastModified();
            return remoteModifiedTime <= localModifiedTime;
        }


    }


    public void updateProxySettings() {
        boolean useProxy;
        String proxyHost;
        int proxyPort = -1;
        boolean auth = false;
        String user = null;
        String pw = null;

        PreferenceManager prefMgr = PreferenceManager.getInstance();
        useProxy = prefMgr.getAsBoolean(PreferenceManager.USE_PROXY);
        proxyHost = prefMgr.get(PreferenceManager.PROXY_HOST, null);
        try {
            proxyPort = Integer.parseInt(prefMgr.get(PreferenceManager.PROXY_PORT, "-1"));
        } catch (NumberFormatException e) {
            proxyPort = -1;
        }
        auth = prefMgr.getAsBoolean(PreferenceManager.PROXY_AUTHENTICATE);
        user = prefMgr.get(PreferenceManager.PROXY_USER, null);
        String pwString = prefMgr.get(PreferenceManager.PROXY_PW, null);
        if (pwString != null) {
            pw = Utilities.base64Decode(pwString);
        }

        String proxyTypeString = prefMgr.get(PreferenceManager.PROXY_TYPE, "HTTP");
        Proxy.Type type = proxyTypeString.equals("SOCKS") ? Proxy.Type.SOCKS : Proxy.Type.HTTP;

        proxySettings = new ProxySettings(useProxy, user, pw, auth, proxyHost, proxyPort, type);
    }

    /**
     * Get the system defined proxy defined for the URI, or null if
     * not available. May also return a {@code Proxy} object which
     * represents a direct connection
     *
     * @param uri
     * @return
     */
    private Proxy getSystemProxy(String uri) {
        try {
            ProxySelector selector = ProxySelector.getDefault();
            List<Proxy> proxyList = selector.select(new URI(uri));
            return proxyList.get(0);
        } catch (URISyntaxException e) {
            log.error(e.getMessage(), e);
            return null;
        } catch (NullPointerException e) {
            return null;
        }

    }

    public boolean downloadFile(String url, File outputFile) throws IOException {

        log.info("Downloading " + url + " to " + outputFile.getAbsolutePath());

        HttpURLConnection conn = openConnection(new URL(url), null);

        long contentLength = -1;
        String contentLengthString = conn.getHeaderField("Content-Length");
        if (contentLengthString != null) {
            contentLength = Long.parseLong(contentLengthString);
        }


        log.info("Content length = " + contentLength);

        InputStream is = null;
        OutputStream out = null;

        try {
            is = conn.getInputStream();
            out = new FileOutputStream(outputFile);

            byte[] buf = new byte[64 * 1024];
            int downloaded = 0;
            int bytesRead = 0;
            while ((bytesRead = is.read(buf)) != -1) {
                out.write(buf, 0, bytesRead);
                downloaded += bytesRead;
            }
            log.info("Download complete.  Total bytes downloaded = " + downloaded);
        } finally {
            if (is != null) is.close();
            if (out != null) {
                out.flush();
                out.close();
            }
        }
        long fileLength = outputFile.length();

        return contentLength <= 0 || contentLength == fileLength;
    }


    public void uploadGenomeSpaceFile(String uri, File file, Map<String, String> headers) throws IOException {

        HttpURLConnection urlconnection = null;
        OutputStream bos = null;

        URL url = new URL(uri);
        urlconnection = openConnection(url, headers, "PUT");
        urlconnection.setDoOutput(true);
        urlconnection.setDoInput(true);

        bos = new BufferedOutputStream(urlconnection.getOutputStream());
        BufferedInputStream bis = new BufferedInputStream(new FileInputStream(file));
        int i;
        // read byte by byte until end of stream
        while ((i = bis.read()) > 0) {
            bos.write(i);
        }
        bos.close();
        int responseCode = urlconnection.getResponseCode();

        // Error messages below.
        if (responseCode >= 400) {
            String message = readErrorStream(urlconnection);
            throw new IOException("Error uploading " + file.getName() + " : " + message);
        }
    }


    public String createGenomeSpaceDirectory(URL url, String body) throws IOException {

        HttpURLConnection urlconnection = null;
        OutputStream bos = null;

        Map<String, String> headers = new HashMap<String, String>();
        headers.put("Content-Type", "application/json");
        headers.put("Content-Length", String.valueOf(body.getBytes().length));

        urlconnection = openConnection(url, headers, "PUT");
        urlconnection.setDoOutput(true);
        urlconnection.setDoInput(true);

        bos = new BufferedOutputStream(urlconnection.getOutputStream());
        bos.write(body.getBytes());
        bos.close();
        int responseCode = urlconnection.getResponseCode();

        // Error messages below.
        StringBuffer buf = new StringBuffer();
        InputStream inputStream;

        if (responseCode >= 200 && responseCode < 300) {
            inputStream = urlconnection.getInputStream();
        } else {
            inputStream = urlconnection.getErrorStream();
        }
        BufferedReader br = new BufferedReader(new InputStreamReader(inputStream));
        String nextLine;
        while ((nextLine = br.readLine()) != null) {
            buf.append(nextLine);
            buf.append('\n');
        }
        inputStream.close();

        if (responseCode >= 200 && responseCode < 300) {
            return buf.toString();
        } else {
            throw new IOException("Error creating GS directory: " + buf.toString());
        }
    }

    /**
     * Code for disabling SSL certification
     */
    private void disableCertificateValidation() {
        // Create a trust manager that does not validate certificate chains
        TrustManager[] trustAllCerts = new TrustManager[]{
                new X509TrustManager() {
                    public java.security.cert.X509Certificate[] getAcceptedIssuers() {
                        return new java.security.cert.X509Certificate[0];
                    }

                    public void checkClientTrusted(
                            java.security.cert.X509Certificate[] certs, String authType) {
                    }

                    public void checkServerTrusted(
                            java.security.cert.X509Certificate[] certs, String authType) {
                    }
                }
        };

        // Install the all-trusting trust manager
        try {
            SSLContext sc = SSLContext.getInstance("SSL");
            sc.init(null, trustAllCerts, null);
            HttpsURLConnection.setDefaultSSLSocketFactory(sc.getSocketFactory());
        } catch (NoSuchAlgorithmException e) {
        } catch (KeyManagementException e) {
        }

    }

    private String readContents(InputStream is) throws IOException {
        BufferedInputStream bis = new BufferedInputStream(is);
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        int b;
        while ((b = bis.read()) >= 0) {
            bos.write(b);
        }
        return new String(bos.toByteArray());
    }

    private String readErrorStream(HttpURLConnection connection) throws IOException {
        InputStream inputStream = null;

        try {
            inputStream = connection.getErrorStream();
            if (inputStream == null) {
                return null;
            }
            return readContents(inputStream);
        } finally {
            if (inputStream != null) inputStream.close();
        }


    }

    public HttpURLConnection delete(URL url) throws IOException {
        return openConnection(url, Collections.<String, String>emptyMap(), "DELETE");
    }

    private HttpURLConnection openConnection(URL url, Map<String, String> requestProperties) throws IOException {
        return openConnection(url, requestProperties, "GET");
    }

    private HttpURLConnection openConnection(URL url, Map<String, String> requestProperties, String method) throws IOException {
        return openConnection(url, requestProperties, method, 0);
    }

    /**
     * The "real" connection method
     *
     * @param url
     * @param requestProperties
     * @param method
     * @return
     * @throws java.io.IOException
     */
    private HttpURLConnection openConnection(
            URL url, Map<String, String> requestProperties, String method, int redirectCount) throws IOException {

        //Encode query string portions
        url = StringUtils.encodeURLQueryString(url);
        if (log.isTraceEnabled()) {
            log.trace(url);
        }

        //Encode base portions. Right now just spaces, most common case
        //TODO This is a hack and doesn't work for all characters which need it
        if (StringUtils.countChar(url.toExternalForm(), ' ') > 0) {
            String newPath = url.toExternalForm().replaceAll(" ", "%20");
            url = new URL(newPath);
        }

        Proxy sysProxy = getSystemProxy(url.toExternalForm());
        boolean igvProxySettingsExist = proxySettings != null && proxySettings.useProxy && proxySettings.proxyHost != null && proxySettings.proxyPort > 0;
        boolean useProxy = sysProxy != null || igvProxySettingsExist;

        HttpURLConnection conn;
        if (useProxy) {
            Proxy proxy = sysProxy;
            if (igvProxySettingsExist) {
                proxy = new Proxy(proxySettings.type, new InetSocketAddress(proxySettings.proxyHost, proxySettings.proxyPort));
            }
            conn = (HttpURLConnection) url.openConnection(proxy);

            if (igvProxySettingsExist && proxySettings.auth && proxySettings.user != null && proxySettings.pw != null) {
                byte[] bytes = (proxySettings.user + ":" + proxySettings.pw).getBytes();

                String encodedUserPwd = String.valueOf(Base64Coder.encode(bytes));
                conn.setRequestProperty("Proxy-Authorization", "Basic " + encodedUserPwd);
            }
        } else {
            conn = (HttpURLConnection) url.openConnection();
        }

        if (GSUtils.isGenomeSpace(url)) {
            conn.setRequestProperty("Accept", "application/json,text/plain");
        } else {
            conn.setRequestProperty("Accept", "text/plain");
        }

        //------//
        //There seems to be a bug with JWS caches
        //So we avoid caching

        //This default is persistent, really should be available statically but isn't
        conn.setDefaultUseCaches(false);
        conn.setUseCaches(false);
        //------//


        conn.setConnectTimeout(Globals.CONNECT_TIMEOUT);
        conn.setReadTimeout(Globals.READ_TIMEOUT);
        conn.setRequestMethod(method);
        conn.setRequestProperty("Connection", "Keep-Alive");
        if (requestProperties != null) {
            for (Map.Entry<String, String> prop : requestProperties.entrySet()) {
                conn.setRequestProperty(prop.getKey(), prop.getValue());
            }
        }
        conn.setRequestProperty("User-Agent", Globals.applicationString());

        if (method.equals("PUT")) {
            return conn;
        } else {

            int code = conn.getResponseCode();

            // Redirects.  These can occur even if followRedirects == true if there is a change in protocol,
            // for example http -> https.
            if (code >= 300 && code < 400) {

                if (redirectCount > MAX_REDIRECTS) {
                    throw new IOException("Too many redirects");
                }

                String newLocation = conn.getHeaderField("Location");
                log.debug("Redirecting to " + newLocation);

                return openConnection(new URL(newLocation), requestProperties, method, redirectCount++);
            }

            // TODO -- handle other response codes.
            else if (code >= 400) {

                String message;
                if (code == 404) {
                    message = "File not found: " + url.toString();
                    throw new FileNotFoundException(message);
                } else if (code == 401) {
                    // Looks like this only happens when user hits "Cancel".
                    // message = "Not authorized to view this file";
                    // JOptionPane.showMessageDialog(null, message, "HTTP error", JOptionPane.ERROR_MESSAGE);
                    redirectCount = MAX_REDIRECTS + 1;
                    return null;
                } else {
                    message = conn.getResponseMessage();
                }
                String details = readErrorStream(conn);
                log.error("URL: " + url.toExternalForm() + ". error stream: " + details);
                log.error("Code: " + code + ". " + message);
                HttpResponseException exc = new HttpResponseException(code);
                throw exc;
            }
        }
        return conn;
    }

    public void setDefaultPassword(String defaultPassword) {
        this.defaultPassword = defaultPassword.toCharArray();
    }

    public void setDefaultUserName(String defaultUserName) {
        this.defaultUserName = defaultUserName;
    }

    public void clearDefaultCredentials() {
        this.defaultPassword = null;
        this.defaultUserName = null;
    }


    /**
     * Test to see if this client can successfully retrieve a portion of a remote file using the byte-range header.
     * This is not a test of the server, but the client.  In some environments the byte-range header gets removed
     * by filters after the request is made by IGV.
     *
     * @return
     */
    public boolean useByteRange(URL url) {

        if (BYTE_RANGE_DISABLED) return false;

        // We can test byte-range success for hosts we can reach.

        final String host = url.getHost();

        if (byteRangeTestMap.containsKey(host)) {
            return byteRangeTestMap.get(host);
        } else {
            SeekableStream str = null;
            try {
                boolean byteRangeTestSuccess = true;

                if (host.contains("broadinstitute.org")) {
                    byteRangeTestSuccess = testBroadHost(host);
                } else {
                    // Non-broad URL
                    int l = (int) Math.min(1000, HttpUtils.getInstance().getContentLength(url));
                    if (l > 1000) {

                        byte[] firstBytes = new byte[l];
                        str = new IGVSeekableHTTPStream(url);
                        str.readFully(firstBytes);

                        int end = firstBytes.length;
                        int start = end - 100;
                        str.seek(start);
                        int len = end - start;
                        byte[] buffer = new byte[len];
                        int n = 0;
                        while (n < len) {
                            int count = str.read(buffer, n, len - n);
                            if (count < 0)
                                throw new EOFException();
                            n += count;
                        }

                        for (int i = 0; i < len; i++) {
                            if (buffer[i] != firstBytes[i + start]) {
                                byteRangeTestSuccess = false;
                                break;
                            }
                        }
                    } else {
                        // Too small a sample to test, return "true" but don't record this host as tested.
                        return true;
                    }
                }

                if (byteRangeTestSuccess) {
                    log.info("Range-byte request succeeded");
                } else {
                    log.info("Range-byte test failed -- problem with client network environment.");
                }

                byteRangeTestMap.put(host, byteRangeTestSuccess);
                return byteRangeTestSuccess;

            } catch (IOException e) {
                log.error("Error while testing byte range " + e.getMessage());
                // We could not reach the test server, so we can't know if this client can do byte-range tests or
                // not.  Take the "optimistic" view.
                return true;
            } finally {
                if (str != null) try {
                    str.close();
                } catch (IOException e) {
                    log.error("Error closing stream (" + url.toExternalForm() + ")", e);
                }
            }

        }
    }

    private boolean testBroadHost(String host) throws IOException {
        // Test broad urls for successful byte range requests.
        log.info("Testing range-byte request on host: " + host);

        String testURL;
        if (host.startsWith("igvdata.broadinstitute.org")) {
            // Amazon cloud front
            testURL = "http://igvdata.broadinstitute.org/genomes/seq/hg19/chr12.txt";
        } else if (host.startsWith("igv.broadinstitute.org")) {
            // Amazon S3
            testURL = "http://igv.broadinstitute.org/genomes/seq/hg19/chr12.txt";
        } else {
            // All others
            testURL = "http://www.broadinstitute.org/igvdata/annotations/seq/hg19/chr12.txt";
        }

        byte[] expectedBytes = {'T', 'C', 'G', 'C', 'T', 'T', 'G', 'A', 'A', 'C', 'C', 'C', 'G', 'G',
                'G', 'A', 'G', 'A', 'G', 'G'};
        IGVSeekableHTTPStream str = null;

        try {
            str = new IGVSeekableHTTPStream(new URL(testURL));

            str.seek(25350000);
            byte[] buffer = new byte[80000];
            str.read(buffer);
            String result = new String(buffer);
            for (int i = 0; i < expectedBytes.length; i++) {
                if (buffer[i] != expectedBytes[i]) {
                    return false;
                }
            }
            return true;
        } finally {
            if (str != null) str.close();
        }
    }


    public void shutdown() {
        // Do any cleanup required here
    }

    /**
     * Checks if the string is a URL (not necessarily remote, can be any protocol)
     *
     * @param f
     * @return
     */
    public static boolean isURL(String f) {
        return f.startsWith("http:") || f.startsWith("ftp:") || f.startsWith("https:") || URLmatcher.matcher(f).matches();
    }

    public static Map<String, String> parseQueryString(String query) {
        String[] params = query.split("&");
        Map<String, String> map = new HashMap<String, String>();
        for (String param : params) {
            String[] name_val = param.split("=", 2);
            map.put(name_val[0], name_val[1]);
        }
        return map;
    }


    public static class ProxySettings {
        boolean auth = false;
        String user;
        String pw;
        boolean useProxy;
        String proxyHost;
        int proxyPort = -1;
        Proxy.Type type;

        public ProxySettings(boolean useProxy, String user, String pw, boolean auth, String proxyHost, int proxyPort) {
            this(useProxy, user, pw, auth, proxyHost, proxyPort, Proxy.Type.HTTP);
            this.auth = auth;
        }

        public ProxySettings(boolean useProxy, String user, String pw, boolean auth, String proxyHost, int proxyPort, Proxy.Type proxyType) {
            this.auth = auth;
            this.proxyHost = proxyHost;
            this.proxyPort = proxyPort;
            this.pw = pw;
            this.useProxy = useProxy;
            this.user = user;
            this.type = proxyType;
        }
    }

    /**
     * The default authenticator
     */
    public class IGVAuthenticator extends Authenticator {

        Hashtable<String, PasswordAuthentication> pwCache = new Hashtable<String, PasswordAuthentication>();
        HashSet<String> cacheAttempts = new HashSet<String>();

        /**
         * Called when password authentication is needed.
         *
         * @return
         */
        @Override
        protected synchronized PasswordAuthentication getPasswordAuthentication() {

            RequestorType type = getRequestorType();
            String urlString = getRequestingURL().toString();
            boolean isProxyChallenge = type == RequestorType.PROXY;

            // Cache user entered PWs.  In normal use this shouldn't be necessary as credentials are cached upstream,
            // but if loading many files in parallel (e.g. from sessions) calls to this method can queue up before the
            // user enters their credentials, causing needless reentry.
            String pKey = type.toString() + getRequestingProtocol() + getRequestingHost();
            PasswordAuthentication pw = pwCache.get(pKey);
            if (pw != null) {
                // Prevents infinite loop if credentials are incorrect
                if (cacheAttempts.contains(urlString)) {
                    cacheAttempts.remove(urlString);
                } else {
                    cacheAttempts.add(urlString);
                    return pw;
                }
            }

            if (isProxyChallenge) {
                if (proxySettings.auth && proxySettings.user != null && proxySettings.pw != null) {
                    return new PasswordAuthentication(proxySettings.user, proxySettings.pw.toCharArray());
                }
            }

            if (defaultUserName != null && defaultPassword != null) {
                return new PasswordAuthentication(defaultUserName, defaultPassword);
            }

            Frame owner = IGV.hasInstance() ? IGV.getMainFrame() : null;

            boolean isGenomeSpace = GSUtils.isGenomeSpace(getRequestingURL());
            if (isGenomeSpace) {
                // If we are being challenged by GS the token must be bad/expired
                GSUtils.logout();
            }

            LoginDialog dlg = new LoginDialog(owner, isGenomeSpace, urlString, isProxyChallenge);
            dlg.setVisible(true);
            if (dlg.isCanceled()) {
                return null;
            } else {
                final String userString = dlg.getUsername();
                final char[] userPass = dlg.getPassword();

                if (isProxyChallenge) {
                    proxySettings.user = userString;
                    proxySettings.pw = new String(userPass);
                }

                pw = new PasswordAuthentication(userString, userPass);
                pwCache.put(pKey, pw);
                return pw;
            }
        }
    }


    /**
     * Provide override for unit tests
     */
    public void setAuthenticator(Authenticator authenticator) {
        Authenticator.setDefault(authenticator);
    }

    /**
     * For unit tests
     */
    public void resetAuthenticator() {
        Authenticator.setDefault(new IGVAuthenticator());

    }


    /**
     * Extension of CookieManager that grabs cookies from the GenomeSpace identity server to store locally.
     * This is to support the GenomeSpace "single sign-on". Examples ...
     * gs-username=igvtest; Domain=.genomespace.org; Expires=Mon, 21-Jul-2031 03:27:23 GMT; Path=/
     * gs-token=HnR9rBShNO4dTXk8cKXVJT98Oe0jWVY+; Domain=.genomespace.org; Expires=Mon, 21-Jul-2031 03:27:23 GMT; Path=/
     */

    static class IGVCookieManager extends CookieManager {

        @Override
        public Map<String, List<String>> get(URI uri, Map<String, List<String>> requestHeaders) throws IOException {
            Map<String, List<String>> headers = new HashMap<String, List<String>>();
            headers.putAll(super.get(uri, requestHeaders));


            if (GSUtils.isGenomeSpace(uri.toURL())) {
                String token = GSUtils.getGSToken();
                if (token != null) {
                    List<String> cookieList = headers.get("Cookie");
                    boolean needsTokenCookie = true;
                    if (cookieList == null) {
                        cookieList = new ArrayList<String>(1);
                        headers.put("Cookie", cookieList);
                    }

                    for (String cookie : cookieList) {
                        if (cookie.startsWith("gs-token")) {
                            needsTokenCookie = false;
                            break;
                        }
                    }
                    if (needsTokenCookie) {
                        cookieList.add("gs-token=" + token);
                    }
                }
            }

            return Collections.unmodifiableMap(headers);
        }

        @Override
        public void put(URI uri, Map<String, List<String>> responseHeaders) throws IOException {
            String urilc = uri.toString().toLowerCase();
            if (urilc.contains("identity") && urilc.contains("genomespace")) {
                List<String> cookies = responseHeaders.get("Set-Cookie");
                if (cookies != null) {
                    for (String cstring : cookies) {
                        List<HttpCookie> cookieList = HttpCookie.parse(cstring);
                        for (HttpCookie cookie : cookieList) {
                            String cookieName = cookie.getName();
                            String value = cookie.getValue();
                            if (cookieName.equals("gs-token")) {
                                //log.debug("gs-token: " + value);
                                GSUtils.setGSToken(value);
                            } else if (cookieName.equals("gs-username")) {
                                //log.debug("gs-username: " + value);
                                GSUtils.setGSUser(value);
                            }
                        }
                    }
                }
            }
            super.put(uri, responseHeaders);
        }
    }

}
