taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/config/BioCataloguePluginConfigurationPanel.java - incubator-taverna-workbench - Git at Google

 package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.config;

 import java.awt.Font;
 import java.awt.GridBagConstraints;
 import java.awt.GridBagLayout;
 import java.awt.Insets;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
 import java.net.ProxySelector;
 import java.net.URL;

 import javax.swing.BorderFactory;
 import javax.swing.JButton;
 import javax.swing.JFrame;
 import javax.swing.JLabel;
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JTextArea;
 import javax.swing.JTextField;

 import org.apache.http.HttpEntity;
 import org.apache.http.HttpResponse;
 import org.apache.http.auth.AuthScope;
 import org.apache.http.auth.UsernamePasswordCredentials;
 //import org.apache.http.client.HttpClient;
 import org.apache.http.client.methods.HttpGet;
 import org.apache.http.impl.client.DefaultHttpClient;
 import org.apache.http.impl.conn.ProxySelectorRoutePlanner;
 import org.apache.http.protocol.BasicHttpContext;
 import org.apache.http.protocol.HttpContext;
 import org.apache.log4j.Logger;
 import org.jdom.Attribute;
 import org.jdom.Document;
 import org.jdom.input.SAXBuilder;

 import net.sf.taverna.biocatalogue.model.connectivity.BioCatalogueClient;
 import net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponentFactory;


 /**
  *
  * @author Sergejs Aleksejevs
  */
 @SuppressWarnings("serial")
 public class BioCataloguePluginConfigurationPanel extends JPanel
 {
 	public static final String APPLICATION_XML_MIME_TYPE = "application/xml";

 	public static String PROXY_HOST = "http.proxyHost";
 	public static String PROXY_PORT = "http.proxyPort";
 	public static String PROXY_USERNAME = "http.proxyUser";
 	public static String PROXY_PASSWORD = "http.proxyPassword";

 	// 1.0.0b and higher until the first digit changes, as according to "Semantic Versioning"
 	// from http://www.biocatalogue.org/wiki/doku.php?id=public:api:changelog
 	// "Major version X (X.y.z | X > 0) MUST be incremented if any backwards
 	// incompatible changes are introduced to the public API. It MAY include minor and patch level changes."
 	public static String[] MIN_SUPPORTED_BIOCATALOGUE_API_VERSION = {"1", "1", "0"}; // major, minor and patch versions
 	public static String API_VERSION = "apiVersion";

 	private BioCataloguePluginConfiguration configuration =
                           BioCataloguePluginConfiguration.getInstance();


 	// UI elements
 	JTextField tfBioCatalogueAPIBaseURL;

 	private Logger logger = Logger.getLogger(BioCataloguePluginConfigurationPanel.class);

 	public BioCataloguePluginConfigurationPanel() {
 		initialiseUI();
 		resetFields();
 	}

   private void initialiseUI()
   {
     this.setLayout(new GridBagLayout());
     GridBagConstraints c = new GridBagConstraints();
     c.fill = GridBagConstraints.HORIZONTAL;
     c.anchor = GridBagConstraints.NORTHWEST;
     c.weightx = 1.0;

     c.gridx = 0;
     c.gridy = 0;
     JTextArea taDescription = new JTextArea("Configure the Service Catalogue integration functionality");
     taDescription.setFont(taDescription.getFont().deriveFont(Font.PLAIN, 11));
     taDescription.setLineWrap(true);
     taDescription.setWrapStyleWord(true);
     taDescription.setEditable(false);
     taDescription.setFocusable(false);
     taDescription.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));
     this.add(taDescription, c);


     c.gridy++;
     c.insets = new Insets(20, 0, 0, 0);
     JLabel jlBioCatalogueAPIBaseURL = new JLabel("Base URL of the Service Catalogue instance to connect to:");
     this.add(jlBioCatalogueAPIBaseURL, c);

     c.gridy++;
     c.insets = new Insets(0, 0, 0, 0);
     tfBioCatalogueAPIBaseURL = new JTextField();
     this.add(tfBioCatalogueAPIBaseURL, c);


     c.gridy++;
     c.insets = new Insets(30, 0, 0, 0);
     // We are not removing BioCatalogue services from its config panel any more -
     // they are being handled by the Taverna's Service Registry
 //    JButton bForgetStoredServices = new JButton("Forget services added to Service Panel by BioCatalogue Plugin");
 //    bForgetStoredServices.addActionListener(new ActionListener() {
 //      public void actionPerformed(ActionEvent e)
 //      {
 //        int response = JOptionPane.showConfirmDialog(null, // no way T2ConfigurationFrame instance can be obtained to be used as a parent...
 //                                       "Are you sure you want to clear all SOAP operations and REST methods\n" +
 //                                       "that were added to the Service Panel by the BioCatalogue Plugin?\n\n" +
 //                                       "This action is permanent is cannot be undone.\n\n" +
 //                                       "Do you want to proceed?", "BioCatalogue Plugin", JOptionPane.YES_NO_OPTION);
 //
 //        if (response == JOptionPane.YES_OPTION)
 //        {
 //          BioCatalogueServiceProvider.clearRegisteredServices();
 //          JOptionPane.showMessageDialog(null,  // no way T2ConfigurationFrame instance can be obtained to be used as a parent...
 //                          "Stored services have been successfully cleared, but will remain\n" +
 //                          "being shown in Service Panel during this session.\n\n" +
 //                          "They will not appear in the Service Panel after you restart Taverna.",
 //                          "BioCatalogue Plugin", JOptionPane.INFORMATION_MESSAGE);
 //        }
 //      }
 //    });
 //    this.add(bForgetStoredServices, c);


     JButton bLoadDefaults = new JButton("Load Defaults");
     bLoadDefaults.addActionListener(new ActionListener() {
       public void actionPerformed(ActionEvent e) {
         loadDefaults();
       }
     });

     JButton bReset = new JButton("Reset");
     bReset.addActionListener(new ActionListener() {
       public void actionPerformed(ActionEvent e) {
         resetFields();
       }
     });

     JButton bApply = new JButton("Apply");
     bApply.addActionListener(new ActionListener() {
       public void actionPerformed(ActionEvent e) {
         applyChanges();
       }
     });

     JPanel jpActionButtons = new JPanel();
     jpActionButtons.add(bLoadDefaults);
     jpActionButtons.add(bReset);
     jpActionButtons.add(bApply);
     c.insets = new Insets(30, 0, 0, 0);
     c.gridy++;
     c.weighty = 1.0;
     this.add(jpActionButtons, c);
   }


   /**
    * Resets all fields to the last saved configuration.
    */
   private void resetFields() {
     tfBioCatalogueAPIBaseURL.setText(configuration.getProperty(BioCataloguePluginConfiguration.SERVICE_CATALOGUE_BASE_URL));
   }

   /**
    * Resets all fields to the default values.
    */
   private void loadDefaults() {
     tfBioCatalogueAPIBaseURL.setText(configuration.getDefaultProperty(BioCataloguePluginConfiguration.SERVICE_CATALOGUE_BASE_URL));
   }

   /**
    * Saves recent changes to the configuration parameter map.
    * Some input validation is performed as well.
    */
 	private void applyChanges() {
 		// --- BioCatalogue BASE URL ---

 		String candidateBaseURL = tfBioCatalogueAPIBaseURL.getText();
 		if (candidateBaseURL.length() == 0) {
 			JOptionPane.showMessageDialog(this,
 					"Service Catalogue base URL must not be blank",
 					"Service Catalogue Configuration", JOptionPane.WARNING_MESSAGE);
 			tfBioCatalogueAPIBaseURL.requestFocusInWindow();
 			return;
 		} else {
 			try {
 				new URL(candidateBaseURL);
 			} catch (MalformedURLException e) {
 				JOptionPane
 						.showMessageDialog(
 								this,
 								"Currently set Service Catalogue instance URL is not valid\n." +
 								"Please check the URL and try again.",
 								"Service Catalogue Configuration",
 								JOptionPane.WARNING_MESSAGE);
 				tfBioCatalogueAPIBaseURL.selectAll();
 				tfBioCatalogueAPIBaseURL.requestFocusInWindow();
 				return;
 			}

 			// check if the base URL has changed from the last saved state
 			if (!candidateBaseURL
 					.equals(configuration
 							.getProperty(BioCataloguePluginConfiguration.SERVICE_CATALOGUE_BASE_URL))) {
 					// Perform various checks on the new URL

 				// Do a GET with "Accept" header set to "application/xml"
 				// We are expecting a 200 OK and an XML doc in return that
 				// contains the BioCataogue version number element.
 				DefaultHttpClient httpClient = new DefaultHttpClient();

 				// Set the proxy settings, if any
 				if (System.getProperty(PROXY_HOST) != null
 						&& !System.getProperty(PROXY_HOST).equals("")) {
 					// Instruct HttpClient to use the standard
 					// JRE proxy selector to obtain proxy information
 					ProxySelectorRoutePlanner routePlanner = new ProxySelectorRoutePlanner(
 							httpClient.getConnectionManager().getSchemeRegistry(), ProxySelector
 									.getDefault());
 					httpClient.setRoutePlanner(routePlanner);
 					// Do we need to authenticate the user to the proxy?
 					if (System.getProperty(PROXY_USERNAME) != null
 							&& !System.getProperty(PROXY_USERNAME).equals("")) {
 						// Add the proxy username and password to the list of credentials
 						httpClient.getCredentialsProvider().setCredentials(
 								new AuthScope(System.getProperty(PROXY_HOST),Integer.parseInt(System.getProperty(PROXY_PORT))),
 								new UsernamePasswordCredentials(System.getProperty(PROXY_USERNAME), System.getProperty(PROXY_PASSWORD)));
 					}
 				}

 				HttpGet httpGet = new HttpGet(candidateBaseURL);
 				httpGet.setHeader("Accept", APPLICATION_XML_MIME_TYPE);

 				// Execute the request
 				HttpContext localContext = new BasicHttpContext();
 				HttpResponse httpResponse;
 				try {
 					httpResponse = httpClient.execute(httpGet, localContext);
 				} catch (Exception ex1) {
 					logger.error("Service Catalogue preferences configuration: Failed to do "
 							+ httpGet.getRequestLine(), ex1);
 					// Warn the user
 					JOptionPane.showMessageDialog(this,
 							"Failed to connect to the URL of the Service Catalogue instance.\n"
 									+ "Please check the URL and try again.",
 							"Service Catalogue Configuration",
 							JOptionPane.INFORMATION_MESSAGE);

 					// Release resource
 					httpClient.getConnectionManager().shutdown();

 					tfBioCatalogueAPIBaseURL.requestFocusInWindow();
 					return;
 				}

 				if (httpResponse.getStatusLine().getStatusCode() == HttpURLConnection.HTTP_OK) { // HTTP/1.1 200 OK
 					HttpEntity httpEntity = httpResponse.getEntity();
 					String contentType = httpEntity.getContentType().getValue()
 							.toLowerCase().trim();
 					logger
 							.info("Service Catalogue preferences configuration: Got 200 OK when testing the Service Catalogue instance by doing "
 									+ httpResponse.getStatusLine()
 									+ ". Content type of response "
 									+ contentType);
 					if (contentType.startsWith(APPLICATION_XML_MIME_TYPE)) {
 						String value = null;
 						Document doc = null;
 						try {
 							value = readResponseBodyAsString(httpEntity)
 									.trim();
 							// Try to read this string into an XML document
 							SAXBuilder builder = new SAXBuilder();
 							byte[] bytes = value.getBytes("UTF-8");
 							doc = builder.build(new ByteArrayInputStream(bytes));
 						} catch (Exception ex2) {
 							logger.error("Service Catalogue preferences configuration: Failed to build an XML document from the response.", ex2);
 							// Warn the user
 							JOptionPane.showMessageDialog(this,
 									"Failed to get the expected response body when testing the Service Catalogue instance.\n"
 											+ "The URL is probably wrong. Please check it and try again.",
 									"Service Catalogue Configuration",
 									JOptionPane.INFORMATION_MESSAGE);
 							tfBioCatalogueAPIBaseURL.requestFocusInWindow();
 							return;
 						}
 						finally{
 							// Release resource
 							httpClient.getConnectionManager().shutdown();
 						}
 						// Get the version element from the XML document
 						Attribute apiVersionAttribute = doc.getRootElement().getAttribute(API_VERSION);
 						if (apiVersionAttribute != null){
 							String apiVersion = apiVersionAttribute.getValue();
 							String versions[] = apiVersion.split("[.]");
 							String majorVersion = versions[0];
 							String minorVersion = versions[1];
 							try {
 							//String patchVersion = versions[2]; // we are not comparing the patch versions
 							String supportedMajorVersion = MIN_SUPPORTED_BIOCATALOGUE_API_VERSION[0];
 							String supportedMinorVersion = MIN_SUPPORTED_BIOCATALOGUE_API_VERSION[1];
 							Integer iSupportedMajorVersion = Integer.parseInt(supportedMajorVersion);
 							Integer iMajorVersion = Integer.parseInt(majorVersion);
 							Integer iSupportedMinorVersion = Integer.parseInt(supportedMinorVersion);
 							Integer iMinorVersion = Integer.parseInt(minorVersion);
 							if (!(iSupportedMajorVersion == iMajorVersion &&
 									iSupportedMinorVersion <= iMinorVersion)){
 								// Warn the user
 								JOptionPane
 										.showMessageDialog(
 												this,
 												"The version of the Service Catalogue instance you are trying to connect to is not supported.\n"
 														+ "Please change the URL and try again.",
 												"Service Catalogue Configuration",
 												JOptionPane.INFORMATION_MESSAGE);
 								tfBioCatalogueAPIBaseURL.requestFocusInWindow();
 								return;
 							}
 							} catch (Exception e) {
 								logger.error(e);
 							}
 						} // if null - we'll try to do our best to connect to BioCatalogue anyway
 					} else {
 						logger
 								.error("Service Catalogue preferences configuration: Failed to get the expected response content type when testing the Service Catalogue instance. "
 										+ httpGet.getRequestLine()
 										+ " returned content type '"
 										+ contentType
 										+ "'; expected response content type is 'application/xml'.");
 						// Warn the user
 						JOptionPane
 								.showMessageDialog(
 										this,
 										"Failed to get the expected response content type when testing the Service Catalogue instance.\n"
 										+ "The URL is probably wrong. Please check it and try again.",
 										"Service Catalogue Plugin",
 										JOptionPane.INFORMATION_MESSAGE);
 						tfBioCatalogueAPIBaseURL.requestFocusInWindow();
 						return;
 					}
 				}
 				else{
 					logger
 							.error("Service Catalogue preferences configuration: Failed to get the expected response status code when testing the Service Catalogue instance. "
 									+ httpGet.getRequestLine()
 									+ " returned the status code "
 									+ httpResponse.getStatusLine()
 											.getStatusCode() + "; expected status code is 200 OK.");
 					// Warn the user
 					JOptionPane
 							.showMessageDialog(
 									this,
 									"Failed to get the expected response status code when testing the Service Catalogue instance.\n"
 									+ "The URL is probably wrong. Please check it and try again.",
 									"Service Catalogue Configuration",
 									JOptionPane.INFORMATION_MESSAGE);
 					tfBioCatalogueAPIBaseURL.requestFocusInWindow();
 					return;
 				}

 				// Warn the user of the changes in the BioCatalogue base URL
 				JOptionPane
 						.showMessageDialog(
 								this,
 								"You have updated the Service Catalogue base URL.\n"
 										+ "This does not take effect until you restart Taverna.",
 										"Service catalogue Configuration",
 								JOptionPane.INFORMATION_MESSAGE);

 			}

 			// the new base URL seems to be valid - can save it into config
 			// settings
 			configuration.setProperty(
 					BioCataloguePluginConfiguration.SERVICE_CATALOGUE_BASE_URL,
 					candidateBaseURL);

 /*			// also update the base URL in the BioCatalogueClient
 			BioCatalogueClient.getInstance()
 					.setBaseURL(candidateBaseURL);*/
 		}

 	}


   /**
    * For testing only.
    */
   public static void main(String[] args) {
     JFrame theFrame = new JFrame();
     theFrame.add(new BioCataloguePluginConfigurationPanel());
     theFrame.pack();
     theFrame.setLocationRelativeTo(null);
     theFrame.setVisible(true);
   }

 	/**
 	 * Worker method that extracts the content of the received HTTP message as a
 	 * string. It also makes use of the charset that is specified in the
 	 * Content-Type header of the received data to read it appropriately.
 	 *
 	 * @param entity
 	 * @return
 	 * @throws IOException
 	 */
 	// Taken from HTTPRequestHandler in rest-activity by Sergejs Aleksejevs
 	private static String readResponseBodyAsString(HttpEntity entity)
 			throws IOException {
 		// get charset name
 		String charset = null;
 		String contentType = entity.getContentType().getValue().toLowerCase();

 		String[] contentTypeParts = contentType.split(";");
 		for (String contentTypePart : contentTypeParts) {
 			contentTypePart = contentTypePart.trim();
 			if (contentTypePart.startsWith("charset=")) {
 				charset = contentTypePart.substring("charset=".length());
 			}
 		}

 		// read the data line by line
 		StringBuilder responseBodyString = new StringBuilder();
 		BufferedReader reader = new BufferedReader(new InputStreamReader(entity
 				.getContent(), charset));

 		String str;
 		while ((str = reader.readLine()) != null) {
 			responseBodyString.append(str + "\n");
 		}

 		return (responseBodyString.toString());
 	}

 }
	package net.sf.taverna.t2.ui.perspectives.biocatalogue.integration.config;

	import java.awt.Font;
	import java.awt.GridBagConstraints;
	import java.awt.GridBagLayout;
	import java.awt.Insets;
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.io.BufferedReader;
	import java.io.ByteArrayInputStream;
	import java.io.IOException;
	import java.io.InputStreamReader;
	import java.net.HttpURLConnection;
	import java.net.MalformedURLException;
	import java.net.ProxySelector;
	import java.net.URL;

	import javax.swing.BorderFactory;
	import javax.swing.JButton;
	import javax.swing.JFrame;
	import javax.swing.JLabel;
	import javax.swing.JOptionPane;
	import javax.swing.JPanel;
	import javax.swing.JTextArea;
	import javax.swing.JTextField;

	import org.apache.http.HttpEntity;
	import org.apache.http.HttpResponse;
	import org.apache.http.auth.AuthScope;
	import org.apache.http.auth.UsernamePasswordCredentials;
	//import org.apache.http.client.HttpClient;
	import org.apache.http.client.methods.HttpGet;
	import org.apache.http.impl.client.DefaultHttpClient;
	import org.apache.http.impl.conn.ProxySelectorRoutePlanner;
	import org.apache.http.protocol.BasicHttpContext;
	import org.apache.http.protocol.HttpContext;
	import org.apache.log4j.Logger;
	import org.jdom.Attribute;
	import org.jdom.Document;
	import org.jdom.input.SAXBuilder;

	import net.sf.taverna.biocatalogue.model.connectivity.BioCatalogueClient;
	import net.sf.taverna.t2.ui.perspectives.biocatalogue.MainComponentFactory;


	/**
	*
	* @author Sergejs Aleksejevs
	*/
	@SuppressWarnings("serial")
	public class BioCataloguePluginConfigurationPanel extends JPanel
	{
	public static final String APPLICATION_XML_MIME_TYPE = "application/xml";

	public static String PROXY_HOST = "http.proxyHost";
	public static String PROXY_PORT = "http.proxyPort";
	public static String PROXY_USERNAME = "http.proxyUser";
	public static String PROXY_PASSWORD = "http.proxyPassword";

	// 1.0.0b and higher until the first digit changes, as according to "Semantic Versioning"
	// from http://www.biocatalogue.org/wiki/doku.php?id=public:api:changelog
	// "Major version X (X.y.z \| X > 0) MUST be incremented if any backwards
	// incompatible changes are introduced to the public API. It MAY include minor and patch level changes."
	public static String[] MIN_SUPPORTED_BIOCATALOGUE_API_VERSION = {"1", "1", "0"}; // major, minor and patch versions
	public static String API_VERSION = "apiVersion";

	private BioCataloguePluginConfiguration configuration =
	BioCataloguePluginConfiguration.getInstance();


	// UI elements
	JTextField tfBioCatalogueAPIBaseURL;

	private Logger logger = Logger.getLogger(BioCataloguePluginConfigurationPanel.class);

	public BioCataloguePluginConfigurationPanel() {
	initialiseUI();
	resetFields();
	}

	private void initialiseUI()
	{
	this.setLayout(new GridBagLayout());
	GridBagConstraints c = new GridBagConstraints();
	c.fill = GridBagConstraints.HORIZONTAL;
	c.anchor = GridBagConstraints.NORTHWEST;
	c.weightx = 1.0;

	c.gridx = 0;
	c.gridy = 0;
	JTextArea taDescription = new JTextArea("Configure the Service Catalogue integration functionality");
	taDescription.setFont(taDescription.getFont().deriveFont(Font.PLAIN, 11));
	taDescription.setLineWrap(true);
	taDescription.setWrapStyleWord(true);
	taDescription.setEditable(false);
	taDescription.setFocusable(false);
	taDescription.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));
	this.add(taDescription, c);


	c.gridy++;
	c.insets = new Insets(20, 0, 0, 0);
	JLabel jlBioCatalogueAPIBaseURL = new JLabel("Base URL of the Service Catalogue instance to connect to:");
	this.add(jlBioCatalogueAPIBaseURL, c);

	c.gridy++;
	c.insets = new Insets(0, 0, 0, 0);
	tfBioCatalogueAPIBaseURL = new JTextField();
	this.add(tfBioCatalogueAPIBaseURL, c);


	c.gridy++;
	c.insets = new Insets(30, 0, 0, 0);
	// We are not removing BioCatalogue services from its config panel any more -
	// they are being handled by the Taverna's Service Registry
	// JButton bForgetStoredServices = new JButton("Forget services added to Service Panel by BioCatalogue Plugin");
	// bForgetStoredServices.addActionListener(new ActionListener() {
	// public void actionPerformed(ActionEvent e)
	// {
	// int response = JOptionPane.showConfirmDialog(null, // no way T2ConfigurationFrame instance can be obtained to be used as a parent...
	// "Are you sure you want to clear all SOAP operations and REST methods\n" +
	// "that were added to the Service Panel by the BioCatalogue Plugin?\n\n" +
	// "This action is permanent is cannot be undone.\n\n" +
	// "Do you want to proceed?", "BioCatalogue Plugin", JOptionPane.YES_NO_OPTION);
	//
	// if (response == JOptionPane.YES_OPTION)
	// {
	// BioCatalogueServiceProvider.clearRegisteredServices();
	// JOptionPane.showMessageDialog(null, // no way T2ConfigurationFrame instance can be obtained to be used as a parent...
	// "Stored services have been successfully cleared, but will remain\n" +
	// "being shown in Service Panel during this session.\n\n" +
	// "They will not appear in the Service Panel after you restart Taverna.",
	// "BioCatalogue Plugin", JOptionPane.INFORMATION_MESSAGE);
	// }
	// }
	// });
	// this.add(bForgetStoredServices, c);


	JButton bLoadDefaults = new JButton("Load Defaults");
	bLoadDefaults.addActionListener(new ActionListener() {
	public void actionPerformed(ActionEvent e) {
	loadDefaults();
	}
	});

	JButton bReset = new JButton("Reset");
	bReset.addActionListener(new ActionListener() {
	public void actionPerformed(ActionEvent e) {
	resetFields();
	}
	});

	JButton bApply = new JButton("Apply");
	bApply.addActionListener(new ActionListener() {
	public void actionPerformed(ActionEvent e) {
	applyChanges();
	}
	});

	JPanel jpActionButtons = new JPanel();
	jpActionButtons.add(bLoadDefaults);
	jpActionButtons.add(bReset);
	jpActionButtons.add(bApply);
	c.insets = new Insets(30, 0, 0, 0);
	c.gridy++;
	c.weighty = 1.0;
	this.add(jpActionButtons, c);
	}


	/**
	* Resets all fields to the last saved configuration.
	*/
	private void resetFields() {
	tfBioCatalogueAPIBaseURL.setText(configuration.getProperty(BioCataloguePluginConfiguration.SERVICE_CATALOGUE_BASE_URL));
	}

	/**
	* Resets all fields to the default values.
	*/
	private void loadDefaults() {
	tfBioCatalogueAPIBaseURL.setText(configuration.getDefaultProperty(BioCataloguePluginConfiguration.SERVICE_CATALOGUE_BASE_URL));
	}

	/**
	* Saves recent changes to the configuration parameter map.
	* Some input validation is performed as well.
	*/
	private void applyChanges() {
	// --- BioCatalogue BASE URL ---

	String candidateBaseURL = tfBioCatalogueAPIBaseURL.getText();
	if (candidateBaseURL.length() == 0) {
	JOptionPane.showMessageDialog(this,
	"Service Catalogue base URL must not be blank",
	"Service Catalogue Configuration", JOptionPane.WARNING_MESSAGE);
	tfBioCatalogueAPIBaseURL.requestFocusInWindow();
	return;
	} else {
	try {
	new URL(candidateBaseURL);
	} catch (MalformedURLException e) {
	JOptionPane
	.showMessageDialog(
	this,
	"Currently set Service Catalogue instance URL is not valid\n." +
	"Please check the URL and try again.",
	"Service Catalogue Configuration",
	JOptionPane.WARNING_MESSAGE);
	tfBioCatalogueAPIBaseURL.selectAll();
	tfBioCatalogueAPIBaseURL.requestFocusInWindow();
	return;
	}

	// check if the base URL has changed from the last saved state
	if (!candidateBaseURL
	.equals(configuration
	.getProperty(BioCataloguePluginConfiguration.SERVICE_CATALOGUE_BASE_URL))) {
	// Perform various checks on the new URL

	// Do a GET with "Accept" header set to "application/xml"
	// We are expecting a 200 OK and an XML doc in return that
	// contains the BioCataogue version number element.
	DefaultHttpClient httpClient = new DefaultHttpClient();

	// Set the proxy settings, if any
	if (System.getProperty(PROXY_HOST) != null
	&& !System.getProperty(PROXY_HOST).equals("")) {
	// Instruct HttpClient to use the standard
	// JRE proxy selector to obtain proxy information
	ProxySelectorRoutePlanner routePlanner = new ProxySelectorRoutePlanner(
	httpClient.getConnectionManager().getSchemeRegistry(), ProxySelector
	.getDefault());
	httpClient.setRoutePlanner(routePlanner);
	// Do we need to authenticate the user to the proxy?
	if (System.getProperty(PROXY_USERNAME) != null
	&& !System.getProperty(PROXY_USERNAME).equals("")) {
	// Add the proxy username and password to the list of credentials
	httpClient.getCredentialsProvider().setCredentials(
	new AuthScope(System.getProperty(PROXY_HOST),Integer.parseInt(System.getProperty(PROXY_PORT))),
	new UsernamePasswordCredentials(System.getProperty(PROXY_USERNAME), System.getProperty(PROXY_PASSWORD)));
	}
	}

	HttpGet httpGet = new HttpGet(candidateBaseURL);
	httpGet.setHeader("Accept", APPLICATION_XML_MIME_TYPE);

	// Execute the request
	HttpContext localContext = new BasicHttpContext();
	HttpResponse httpResponse;
	try {
	httpResponse = httpClient.execute(httpGet, localContext);
	} catch (Exception ex1) {
	logger.error("Service Catalogue preferences configuration: Failed to do "
	+ httpGet.getRequestLine(), ex1);
	// Warn the user
	JOptionPane.showMessageDialog(this,
	"Failed to connect to the URL of the Service Catalogue instance.\n"
	+ "Please check the URL and try again.",
	"Service Catalogue Configuration",
	JOptionPane.INFORMATION_MESSAGE);

	// Release resource
	httpClient.getConnectionManager().shutdown();

	tfBioCatalogueAPIBaseURL.requestFocusInWindow();
	return;
	}

	if (httpResponse.getStatusLine().getStatusCode() == HttpURLConnection.HTTP_OK) { // HTTP/1.1 200 OK
	HttpEntity httpEntity = httpResponse.getEntity();
	String contentType = httpEntity.getContentType().getValue()
	.toLowerCase().trim();
	logger
	.info("Service Catalogue preferences configuration: Got 200 OK when testing the Service Catalogue instance by doing "
	+ httpResponse.getStatusLine()
	+ ". Content type of response "
	+ contentType);
	if (contentType.startsWith(APPLICATION_XML_MIME_TYPE)) {
	String value = null;
	Document doc = null;
	try {
	value = readResponseBodyAsString(httpEntity)
	.trim();
	// Try to read this string into an XML document
	SAXBuilder builder = new SAXBuilder();
	byte[] bytes = value.getBytes("UTF-8");
	doc = builder.build(new ByteArrayInputStream(bytes));
	} catch (Exception ex2) {
	logger.error("Service Catalogue preferences configuration: Failed to build an XML document from the response.", ex2);
	// Warn the user
	JOptionPane.showMessageDialog(this,
	"Failed to get the expected response body when testing the Service Catalogue instance.\n"
	+ "The URL is probably wrong. Please check it and try again.",
	"Service Catalogue Configuration",
	JOptionPane.INFORMATION_MESSAGE);
	tfBioCatalogueAPIBaseURL.requestFocusInWindow();
	return;
	}
	finally{
	// Release resource
	httpClient.getConnectionManager().shutdown();
	}
	// Get the version element from the XML document
	Attribute apiVersionAttribute = doc.getRootElement().getAttribute(API_VERSION);
	if (apiVersionAttribute != null){
	String apiVersion = apiVersionAttribute.getValue();
	String versions[] = apiVersion.split("[.]");
	String majorVersion = versions[0];
	String minorVersion = versions[1];
	try {
	//String patchVersion = versions[2]; // we are not comparing the patch versions
	String supportedMajorVersion = MIN_SUPPORTED_BIOCATALOGUE_API_VERSION[0];
	String supportedMinorVersion = MIN_SUPPORTED_BIOCATALOGUE_API_VERSION[1];
	Integer iSupportedMajorVersion = Integer.parseInt(supportedMajorVersion);
	Integer iMajorVersion = Integer.parseInt(majorVersion);
	Integer iSupportedMinorVersion = Integer.parseInt(supportedMinorVersion);
	Integer iMinorVersion = Integer.parseInt(minorVersion);
	if (!(iSupportedMajorVersion == iMajorVersion &&
	iSupportedMinorVersion <= iMinorVersion)){
	// Warn the user
	JOptionPane
	.showMessageDialog(
	this,
	"The version of the Service Catalogue instance you are trying to connect to is not supported.\n"
	+ "Please change the URL and try again.",
	"Service Catalogue Configuration",
	JOptionPane.INFORMATION_MESSAGE);
	tfBioCatalogueAPIBaseURL.requestFocusInWindow();
	return;
	}
	} catch (Exception e) {
	logger.error(e);
	}
	} // if null - we'll try to do our best to connect to BioCatalogue anyway
	} else {
	logger
	.error("Service Catalogue preferences configuration: Failed to get the expected response content type when testing the Service Catalogue instance. "
	+ httpGet.getRequestLine()
	+ " returned content type '"
	+ contentType
	+ "'; expected response content type is 'application/xml'.");
	// Warn the user
	JOptionPane
	.showMessageDialog(
	this,
	"Failed to get the expected response content type when testing the Service Catalogue instance.\n"
	+ "The URL is probably wrong. Please check it and try again.",
	"Service Catalogue Plugin",
	JOptionPane.INFORMATION_MESSAGE);
	tfBioCatalogueAPIBaseURL.requestFocusInWindow();
	return;
	}
	}
	else{
	logger
	.error("Service Catalogue preferences configuration: Failed to get the expected response status code when testing the Service Catalogue instance. "
	+ httpGet.getRequestLine()
	+ " returned the status code "
	+ httpResponse.getStatusLine()
	.getStatusCode() + "; expected status code is 200 OK.");
	// Warn the user
	JOptionPane
	.showMessageDialog(
	this,
	"Failed to get the expected response status code when testing the Service Catalogue instance.\n"
	+ "The URL is probably wrong. Please check it and try again.",
	"Service Catalogue Configuration",
	JOptionPane.INFORMATION_MESSAGE);
	tfBioCatalogueAPIBaseURL.requestFocusInWindow();
	return;
	}

	// Warn the user of the changes in the BioCatalogue base URL
	JOptionPane
	.showMessageDialog(
	this,
	"You have updated the Service Catalogue base URL.\n"
	+ "This does not take effect until you restart Taverna.",
	"Service catalogue Configuration",
	JOptionPane.INFORMATION_MESSAGE);

	}

	// the new base URL seems to be valid - can save it into config
	// settings
	configuration.setProperty(
	BioCataloguePluginConfiguration.SERVICE_CATALOGUE_BASE_URL,
	candidateBaseURL);

	/* // also update the base URL in the BioCatalogueClient
	BioCatalogueClient.getInstance()
	.setBaseURL(candidateBaseURL);*/
	}

	}


	/**
	* For testing only.
	*/
	public static void main(String[] args) {
	JFrame theFrame = new JFrame();
	theFrame.add(new BioCataloguePluginConfigurationPanel());
	theFrame.pack();
	theFrame.setLocationRelativeTo(null);
	theFrame.setVisible(true);
	}

	/**
	* Worker method that extracts the content of the received HTTP message as a
	* string. It also makes use of the charset that is specified in the
	* Content-Type header of the received data to read it appropriately.
	*
	* @param entity
	* @return
	* @throws IOException
	*/
	// Taken from HTTPRequestHandler in rest-activity by Sergejs Aleksejevs
	private static String readResponseBodyAsString(HttpEntity entity)
	throws IOException {
	// get charset name
	String charset = null;
	String contentType = entity.getContentType().getValue().toLowerCase();

	String[] contentTypeParts = contentType.split(";");
	for (String contentTypePart : contentTypeParts) {
	contentTypePart = contentTypePart.trim();
	if (contentTypePart.startsWith("charset=")) {
	charset = contentTypePart.substring("charset=".length());
	}
	}

	// read the data line by line
	StringBuilder responseBodyString = new StringBuilder();
	BufferedReader reader = new BufferedReader(new InputStreamReader(entity
	.getContent(), charset));

	String str;
	while ((str = reader.readLine()) != null) {
	responseBodyString.append(str + "\n");
	}

	return (responseBodyString.toString());
	}

	}