X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fslivkaws%2FSlivkaWSDiscoverer.java;h=7a41431ba8482970085d103b438d50344573f850;hb=076b3b34bc3e02a033213cdac4300444e3c57b74;hp=e9d0d53de2b98ca7dbe84dff83fa317de6cbf5b4;hpb=450e45b30f7bd3913fca34511e534fec955b8195;p=jalview.git

diff --git a/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java b/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
index e9d0d53..7a41431 100644
--- a/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
+++ b/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
@@ -1,36 +1,36 @@
 package jalview.ws.slivkaws;
 
-import jalview.datamodel.AlignmentView;
+import jalview.bin.Cache;
 import jalview.gui.AlignFrame;
-import jalview.ws.WSMenuEntryProviderI;
-import jalview.ws.jws2.MsaWSClient;
+import jalview.ws.WSDiscovererI;
+import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.jws2.PreferredServiceRegistry;
 
-import java.awt.event.ActionEvent;
-import java.io.IOError;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
 import java.io.IOException;
-import java.net.URISyntaxException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
 
 import javax.swing.JMenu;
-import javax.swing.JMenuItem;
 
 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
 
-public class SlivkaWSDiscoverer implements Runnable, WSMenuEntryProviderI
+public class SlivkaWSDiscoverer implements WSDiscovererI
 {
+  private static final String SLIVKA_HOST_URLS = "SLIVKAHOSTURLS";
+
+  private static final String COMPBIO_SLIVKA = "https://www.compbio.dundee.ac.uk/slivka/";
+
   private static SlivkaWSDiscoverer instance = null;
 
-  private SlivkaClient client;
+  private List<ServiceWithParameters> services = List.of();
 
   private SlivkaWSDiscoverer()
   {
-    try
-    {
-      client = new SlivkaClient("gjb-www-1.cluster.lifesci.dundee.ac.uk", 3203);
-    } catch (URISyntaxException e)
-    {
-      throw new RuntimeException(e);
-    }
   }
 
   public static SlivkaWSDiscoverer getInstance()
@@ -42,71 +42,208 @@ public class SlivkaWSDiscoverer implements Runnable, WSMenuEntryProviderI
     return instance;
   }
 
+  private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+      this);
+
   @Override
   public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
   {
     JMenu slivkaMenu = new JMenu("Slivka");
     wsmenu.add(slivkaMenu);
-    JMenu categoryMenu = new JMenu("Alignment");
-    slivkaMenu.add(categoryMenu);
 
-    try
+    JMenu alignmentMenu = new JMenu("Sequence Alignment");
+    slivkaMenu.add(alignmentMenu);
+    JMenu disorderMenu = new JMenu("Protein sequence analysis");
+    slivkaMenu.add(disorderMenu);
+    JMenu conservationMenu = new JMenu("Conservation");
+    slivkaMenu.add(conservationMenu);
+    PreferredServiceRegistry.getRegistry().populateWSMenuEntry(services,
+        changeSupport, slivkaMenu, alignFrame, null);
+
+  }
+
+  volatile boolean ready = false;
+
+  volatile Thread discovererThread = null;
+
+  private class DiscovererThread extends Thread
+  {
+    private Thread oldThread;
+
+    DiscovererThread(Thread oldThread)
+    {
+      super();
+      this.oldThread = oldThread;
+    }
+
+    @Override
+    public void run()
+    {
+      if (oldThread != null)
+      {
+        oldThread.interrupt();
+        try
+        {
+          oldThread.join();
+        } catch (InterruptedException e)
+        {
+          return;
+        } finally
+        {
+          oldThread = null;
+        }
+      }
+      ready = false;
+      reloadServices();
+      ready = !isInterrupted();
+    }
+  }
+
+  Thread discoverer = null;
+
+  @Override
+  public Thread startDiscoverer(PropertyChangeListener changeListener)
+  {
+    changeSupport.addPropertyChangeListener(changeListener);
+    ready = false;
+    (discovererThread = new DiscovererThread(discovererThread)).start();
+    return discovererThread;
+  }
+
+  private void reloadServices()
+  {
+    Cache.log.info("Reloading Slivka services");
+    changeSupport.firePropertyChange("services", services, List.of());
+    ArrayList<ServiceWithParameters> instances = new ArrayList<>();
+
+    for (String url : getServiceUrls())
     {
-      for (SlivkaService service : client.getServices())
+      Cache.log.info(url);
+      SlivkaClient client;
+      client = new SlivkaClient(url);
+      try
       {
-        msaClassifier:
+        for (SlivkaService service : client.getServices())
         {
+          SlivkaWSInstance newinstance = null;
           for (String classifier : service.classifiers)
           {
             if (classifier.contains("Multiple sequence alignment"))
             {
-              break msaClassifier;
+              newinstance = new SlivkaMsaServiceInstance(client, service);
             }
-          }
-          continue;
-        }
-        SlivkaMsaServiceInstance instance = new SlivkaMsaServiceInstance(client, service);
-        JMenuItem defaultEntry = new JMenuItem(String.format("%s with defaults", service.label));
-        defaultEntry.addActionListener((ActionEvent evt) -> {
-          AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-          if (msa != null)
-          {
-            new MsaWSClient(instance, alignFrame.getTitle(), msa, false, true,
-                alignFrame.getViewport().getAlignment().getDataset(), alignFrame);
-          }
-        });
-        categoryMenu.add(defaultEntry);
-
-        JMenuItem customEntry = new JMenuItem(String.format("%s with custom parameters", service.label));
-        customEntry.addActionListener((ActionEvent evt) -> {
-          AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-          if (msa != null)
-          {
-            try
+            if (classifier.contains("Protein sequence analysis")
+                && newinstance == null)
             {
-              SlivkaParamSet paramSet = new SlivkaParamSet(service);
-              new MsaWSClient(instance, paramSet, null, true, alignFrame.getTitle(), msa, false, true,
-                  alignFrame.getViewport().getAlignment().getDataset(), alignFrame);
-            } catch (IOException exc)
+              newinstance = new SlivkaAnnotationServiceInstance(client,
+                  service, false);
+            }
+            if (classifier
+                .contains("Sequence alignment analysis (conservation)"))
             {
-              throw new IOError(exc);
+              newinstance = new SlivkaAnnotationServiceInstance(client,
+                  service, true);
             }
           }
-        });
-        categoryMenu.add(customEntry);
+          if (newinstance != null)
+          {
+            instances.add(newinstance);
+          }
+        }
+      } catch (IOException e)
+      {
+        continue;
+      }
+    }
+
+    services = instances;
+    changeSupport.firePropertyChange("services", List.of(), services);
+
+    Cache.log.info("Slivka services reloading finished");
+  }
+
+  @Override
+  public List<ServiceWithParameters> getServices()
+  {
+    return services;
+  }
+
+  @Override
+  public boolean hasServices()
+  {
+    return ready == true && services.size() > 0;
+  }
+
+  @Override
+  public boolean isRunning()
+  {
+    return discovererThread == null || discovererThread.isAlive()
+        || discovererThread.getState() == Thread.State.NEW;
+  }
+
+  @Override
+  public void setServiceUrls(List<String> wsUrls)
+  {
+    if (wsUrls != null && !wsUrls.isEmpty())
+    {
+      Cache.setProperty(SLIVKA_HOST_URLS, String.join(",", wsUrls));
+    }
+    else
+    {
+      Cache.removeProperty(SLIVKA_HOST_URLS);
+    }
+  }
 
-        categoryMenu.addSeparator();
+  @Override
+  public List<String> getServiceUrls()
+  {
+    String surls = Cache.getDefault(SLIVKA_HOST_URLS, COMPBIO_SLIVKA);
+    String[] urls = surls.split(",");
+    ArrayList<String> valid = new ArrayList<>(urls.length);
+    for (String url : urls)
+    {
+      try
+      {
+        new URL(url);
+        valid.add(url);
+      } catch (MalformedURLException e)
+      {
+        Cache.log.warn("Problem whilst trying to make a URL from '"
+            + ((url != null) ? url : "<null>") + "'");
+        Cache.log.warn(
+            "This was probably due to a malformed comma separated list"
+                + " in the " + SLIVKA_HOST_URLS
+                + " entry of $(HOME)/.jalview_properties)");
+        Cache.log.debug("Exception was ", e);
       }
+    }
+    return valid;
+  }
+
+  @Override
+  public boolean testServiceUrl(URL url)
+  {
+    return getServerStatusFor(url.toString()) == STATUS_OK;
+  }
+
+  @Override
+  public int getServerStatusFor(String url)
+  {
+    try
+    {
+      List<?> services = new SlivkaClient(url).getServices();
+      return services.isEmpty() ? STATUS_NO_SERVICES : STATUS_OK;
     } catch (IOException e)
     {
-      // TODO Auto-generated catch block
-      e.printStackTrace();
+      Cache.log.error("Slivka could not retrieve services list", e);
+      return STATUS_INVALID;
     }
   }
 
   @Override
-  public void run()
+  public String getErrorMessages()
   {
-
+    // TODO Auto-generated method stub
+    return "";
   }
 }