Maintain list of webservices and query any Service Discovery services.

diff --git a/src/jalview/ws/Discoverer.java b/src/jalview/ws/Discoverer.java
new file mode 100755 (executable)
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--- /dev/null
+++ b/src/jalview/ws/Discoverer.java
@@ -0,0 +1,274 @@
+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();
+  }
+}