--- /dev/null
+package jalview.ws;
+
+/**
+ * <p>Title: </p>
+ *
+ * <p>Description: </p>
+ *
+ * <p>Copyright: Copyright (c) 2004</p>
+ *
+ * <p>Company: Dundee University</p>
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+import ext.vamsas.*;
+import java.util.Vector;
+import java.util.Hashtable;
+import java.util.ArrayList;
+
+public class Discoverer
+ extends Thread implements Runnable
+{
+ ext.vamsas.IRegistry registry; // the root registry service.
+ private java.beans.PropertyChangeSupport changeSupport = new java.beans.
+ PropertyChangeSupport(this);
+
+ /**
+ * change listeners are notified of "services" property changes
+ *
+ * @param listener to be added that consumes new services Hashtable object.
+ */
+ public void addPropertyChangeListener(
+ java.beans.PropertyChangeListener listener)
+ {
+ changeSupport.addPropertyChangeListener(listener);
+ }
+
+ /**
+ *
+ *
+ * @param listener to be removed
+ */
+ public void removePropertyChangeListener(
+ java.beans.PropertyChangeListener listener)
+ {
+ changeSupport.removePropertyChangeListener(listener);
+ }
+
+ /**
+ * Property change listener firing routine
+ *
+ * @param prop services
+ * @param oldvalue old services hash
+ * @param newvalue new services hash
+ */
+ public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
+ {
+ changeSupport.firePropertyChange(prop, oldvalue, newvalue);
+ }
+
+ /**
+ * Initializes the server field with a valid service implementation.
+ *
+ * @return true if service was located.
+ */
+ private IRegistry locateWebService(java.net.URL WsURL)
+ {
+ IRegistryServiceLocator loc = new IRegistryServiceLocator(); // Default
+ IRegistry server = null;
+ try
+ {
+ server = loc.getRegistryService(WsURL);
+ ( (RegistryServiceSoapBindingStub) server).setTimeout(60000); // One minute timeout
+ }
+ catch (Exception ex)
+ {
+ jalview.bin.Jalview.log.error(
+ "Serious! Service location failed\nfor URL :" + WsURL +
+ "\n", ex);
+
+ return null;
+ }
+
+ loc.getEngine().setOption("axis", "1");
+
+ return server;
+ }
+
+ static private java.net.URL RootServiceURL = null;
+ static public Vector ServiceURLList = null;
+ static private boolean reallyDiscoverServices = true;
+
+ public static java.util.Hashtable services = null; // vectors of services stored by abstractServiceType string
+ public static java.util.Vector serviceList = null; // flat list of services
+
+ static
+ {
+
+ try
+ {
+ reallyDiscoverServices = jalview.bin.Cache.getDefault("DISCOVER_SERVICES", false);
+ if (reallyDiscoverServices)
+ {
+ RootServiceURL = new java.net.URL(
+ "http://webservices.compbio.dundee.ac.uk:8080/jalTestWS/services/ServiceRegistry");
+ if (ServiceURLList == null)
+ {
+ ServiceURLList = new Vector();
+ }
+ if (!ServiceURLList.contains(RootServiceURL))
+ {
+ ServiceURLList.add(RootServiceURL);
+ }
+ }
+ else
+ {
+ jalview.bin.Jalview.log.debug("Setting default services");
+ services = new Hashtable();
+ // Muscle, Clustal and JPred.
+ ServiceHandle[] defServices = {
+ new ServiceHandle(
+ "MsaWS",
+ "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment " +
+ "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
+ "Muscle Multiple Protein Sequence Alignment"
+),
+ new ServiceHandle(
+ "MsaWS",
+ "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple" +
+ " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice." +
+ " Nucleic Acids Research, 22 4673-4680",
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
+ "ClustalW Multiple Sequence Alignment"),
+ new ServiceHandle(
+ "SecStrPred",
+ "Cuff J. A and Barton G.J (1999) Application of enhanced " +
+ "multiple sequence alignment profiles to improve protein secondary structure prediction, " +
+ "Proteins 40:502-511",
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred","JPred Secondary Structure Prediction"
+ )};
+ services = new Hashtable();
+ serviceList = new Vector();
+ buildServiceLists(defServices, serviceList, services);
+ }
+
+ }
+ catch (Exception e)
+ {
+ System.err.println(
+ "jalview.rootRegistry is not a proper url!\nWas set to " +
+ RootServiceURL + "\n" + e);
+ }
+
+ }
+ // TODO: JBPNote : make this discover more services based on list of
+ // discovery service urls, break cyclic references to the same url and
+ // duplicate service entries (same endpoint *and* same interface)
+ private ServiceHandle[] getServices(java.net.URL location)
+ {
+ ServiceHandles shs = null;
+ try
+ {
+ jalview.bin.Jalview.log.debug("Discovering services using " + location);
+ shs = locateWebService(location).getServices();
+ }
+ catch (Exception e)
+ {
+ System.err.println("failed to locate Services through URL : " +
+ location + "\n");
+ e.printStackTrace();
+
+ }
+ if ( (shs != null) && shs.getServices().length > 0)
+ {
+ return shs.getServices();
+ }
+ return null;
+ }
+
+ /**
+ * Adds a list of services to the service catalog and categorised catalog
+ * returns true if ServiceURLList was modified with a new DiscoveryService URL
+ * @param sh ServiceHandle[]
+ * @param cat Vector
+ * @param sscat Hashtable
+ * @return boolean
+ */
+ static private boolean buildServiceLists(ServiceHandle[] sh, Vector cat,
+ Hashtable sscat)
+ {
+ boolean seenNewDiscovery = false;
+ for (int i = 0, j = sh.length; i < j; i++)
+ {
+ if (!cat.contains(sh[i]))
+ {
+ jalview.bin.Jalview.log.debug("A " + sh[i].getAbstractName() +
+ " service called " +
+ sh[i].getName() + " exists at " +
+ sh[i].getEndpointURL() + "\n");
+ if (!sscat.containsKey(sh[i].getAbstractName()))
+ {
+ sscat.put(sh[i].getAbstractName(), cat = new Vector());
+ }
+ else
+ {
+ cat = (Vector) sscat.get(sh[i].getAbstractName());
+ }
+ cat.add(sh[i]);
+ if (sh[i].getAbstractName().equals("Registry"))
+ {
+ for (int s = 0, sUrls = ServiceURLList.size(); s < sUrls; s++)
+ {
+ java.net.URL disc_serv = null;
+ try
+ {
+ disc_serv = new java.net.URL(sh[i].getEndpointURL());
+ if (!ServiceURLList.contains(disc_serv))
+ {
+ jalview.bin.Jalview.log.debug(
+ "Adding new discovery service at " + disc_serv);
+ ServiceURLList.add(disc_serv);
+ seenNewDiscovery = true;
+ }
+ }
+ catch (Exception e)
+ {
+ jalview.bin.Jalview.log.debug(
+ "Ignoring bad discovery service URL " + sh[i].getEndpointURL(),
+ e);
+ }
+ }
+ }
+ }
+ }
+ return seenNewDiscovery;
+ }
+
+ public void discoverServices()
+ {
+ Hashtable sscat = new Hashtable();
+ Vector cat = new Vector();
+ ServiceHandle sh[] = null;
+ int s_url = 0;
+ if (ServiceURLList==null)
+ {
+ jalview.bin.Jalview.log.debug("No service endpoints to use for service discovery.");
+ return;
+ }
+ while (s_url < ServiceURLList.size())
+ {
+ if ( (sh = getServices( (java.net.URL) ServiceURLList.get(s_url))) != null)
+ {
+
+ buildServiceLists(sh, cat, sscat);
+ }
+ s_url++;
+ }
+ // TODO: decide on correct semantics for services list - PropertyChange
+ // provides a way of passing the new object around
+ // so no need to access original discovery thread.
+ // Curent decision is to change properties then notify listeners with old and new values.
+ Hashtable oldServices = services;
+ Vector oldServicelist = serviceList;
+ services = sscat;
+ serviceList = cat;
+ firePropertyChange("services", oldServices, services);
+ }
+
+ public void run()
+ {
+ discoverServices();
+ }
+}