src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java

   1 package jalview.ws.slivkaws;
   2
   3 import jalview.bin.Cache;
   4 import jalview.gui.AlignFrame;
   5 import jalview.ws.WSDiscovererI;
   6 import jalview.ws.api.ServiceWithParameters;
   7 import jalview.ws.jws2.PreferredServiceRegistry;
   8
   9 import java.beans.PropertyChangeListener;
  10 import java.beans.PropertyChangeSupport;
  11 import java.io.IOException;
  12 import java.net.MalformedURLException;
  13 import java.net.URISyntaxException;
  14 import java.net.URL;
  15 import java.util.ArrayList;
  16 import java.util.List;
  17
  18 import javax.swing.JMenu;
  19
  20 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  21 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  22
  23 public class SlivkaWSDiscoverer implements WSDiscovererI
  24 {
  25   private static final String SLIVKA_HOST_URLS = "SLIVKAHOSTURLS";
  26
  27   private static final String COMPBIO_SLIVKA = "https://www.compbio.dundee.ac.uk/slivka";
  28
  29   private static SlivkaWSDiscoverer instance = null;
  30
  31   private List<ServiceWithParameters> services = List.of();
  32
  33   private SlivkaWSDiscoverer()
  34   {
  35   }
  36
  37   public static SlivkaWSDiscoverer getInstance()
  38   {
  39     if (instance == null)
  40     {
  41       instance = new SlivkaWSDiscoverer();
  42     }
  43     return instance;
  44   }
  45
  46   private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
  47       this);
  48
  49   @Override
  50   public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
  51   {
  52     JMenu slivkaMenu = new JMenu("Slivka");
  53     wsmenu.add(slivkaMenu);
  54
  55     JMenu alignmentMenu = new JMenu("Sequence Alignment");
  56     slivkaMenu.add(alignmentMenu);
  57     JMenu disorderMenu = new JMenu("Protein sequence analysis");
  58     slivkaMenu.add(disorderMenu);
  59     JMenu conservationMenu = new JMenu("Conservation");
  60     slivkaMenu.add(conservationMenu);
  61     PreferredServiceRegistry.getRegistry().populateWSMenuEntry(services,
  62         changeSupport, slivkaMenu, alignFrame, null);
  63
  64   }
  65
  66   volatile boolean ready = false;
  67
  68   volatile Thread discovererThread = null;
  69
  70   private class DiscovererThread extends Thread
  71   {
  72     private Thread oldThread;
  73
  74     DiscovererThread(Thread oldThread)
  75     {
  76       super();
  77       this.oldThread = oldThread;
  78     }
  79
  80     @Override
  81     public void run()
  82     {
  83       if (oldThread != null)
  84       {
  85         oldThread.interrupt();
  86         try
  87         {
  88           oldThread.join();
  89         } catch (InterruptedException e)
  90         {
  91           return;
  92         } finally
  93         {
  94           oldThread = null;
  95         }
  96       }
  97       ready = false;
  98       reloadServices();
  99       ready = !isInterrupted();
 100     }
 101   }
 102
 103   Thread discoverer = null;
 104
 105   @Override
 106   public Thread startDiscoverer(PropertyChangeListener changeListener)
 107   {
 108     changeSupport.addPropertyChangeListener(changeListener);
 109     ready = false;
 110     (discovererThread = new DiscovererThread(discovererThread)).start();
 111     return discovererThread;
 112   }
 113
 114   private void reloadServices()
 115   {
 116     Cache.log.info("Reloading Slivka services");
 117     changeSupport.firePropertyChange("services", services, List.of());
 118     ArrayList<ServiceWithParameters> instances = new ArrayList<>();
 119
 120     for (String url : getServiceUrls())
 121     {
 122       Cache.log.info(url);
 123       SlivkaClient client;
 124       try
 125       {
 126         client = new SlivkaClient(url);
 127       } catch (URISyntaxException e)
 128       {
 129         e.printStackTrace();
 130         continue;
 131       }
 132       try
 133       {
 134         for (SlivkaService service : client.getServices())
 135         {
 136           SlivkaWSInstance newinstance = null;
 137           for (String classifier : service.classifiers)
 138           {
 139             if (classifier.contains("Multiple sequence alignment"))
 140             {
 141               newinstance = new SlivkaMsaServiceInstance(client, service);
 142             }
 143             if (classifier.contains("Protein sequence analysis")
 144                 && newinstance == null)
 145             {
 146               newinstance = new SlivkaAnnotationServiceInstance(client,
 147                   service, false);
 148             }
 149             if (classifier
 150                 .contains("Sequence alignment analysis (conservation)"))
 151             {
 152               newinstance = new SlivkaAnnotationServiceInstance(client,
 153                   service, true);
 154             }
 155           }
 156           if (newinstance != null)
 157           {
 158             instances.add(newinstance);
 159           }
 160         }
 161       } catch (IOException e)
 162       {
 163         continue;
 164       }
 165     }
 166
 167     services = instances;
 168     changeSupport.firePropertyChange("services", List.of(), services);
 169
 170     Cache.log.info("Slivka services reloading finished");
 171   }
 172
 173   @Override
 174   public List<ServiceWithParameters> getServices()
 175   {
 176     return services;
 177   }
 178
 179   @Override
 180   public boolean hasServices()
 181   {
 182     return ready == true && services.size() > 0;
 183   }
 184
 185   @Override
 186   public boolean isRunning()
 187   {
 188     return discovererThread == null || discovererThread.isAlive()
 189         || discovererThread.getState() == Thread.State.NEW;
 190   }
 191
 192   @Override
 193   public void setServiceUrls(List<String> wsUrls)
 194   {
 195     if (wsUrls != null && !wsUrls.isEmpty())
 196     {
 197       Cache.setProperty(SLIVKA_HOST_URLS, String.join(",", wsUrls));
 198     }
 199     else
 200     {
 201       Cache.removeProperty(SLIVKA_HOST_URLS);
 202     }
 203   }
 204
 205   @Override
 206   public List<String> getServiceUrls()
 207   {
 208     String surls = Cache.getDefault(SLIVKA_HOST_URLS, COMPBIO_SLIVKA);
 209     String[] urls = surls.split(",");
 210     ArrayList<String> valid = new ArrayList<>(urls.length);
 211     for (String url : urls)
 212     {
 213       try
 214       {
 215         new URL(url);
 216         valid.add(url);
 217       } catch (MalformedURLException e)
 218       {
 219         Cache.log.warn("Problem whilst trying to make a URL from '"
 220             + ((url != null) ? url : "<null>") + "'");
 221         Cache.log.warn(
 222             "This was probably due to a malformed comma separated list"
 223                 + " in the " + SLIVKA_HOST_URLS
 224                 + " entry of $(HOME)/.jalview_properties)");
 225         Cache.log.debug("Exception was ", e);
 226       }
 227     }
 228     return valid;
 229   }
 230
 231   @Override
 232   public boolean testServiceUrl(URL url)
 233   {
 234     return getServerStatusFor(url.toString()) == STATUS_OK;
 235   }
 236
 237   @Override
 238   public int getServerStatusFor(String url)
 239   {
 240     try
 241     {
 242       List<?> services = new SlivkaClient(url).getServices();
 243       return services.isEmpty() ? STATUS_NO_SERVICES : STATUS_OK;
 244     } catch (IOException | URISyntaxException e)
 245     {
 246       return STATUS_INVALID;
 247     }
 248   }
 249
 250   @Override
 251   public String getErrorMessages()
 252   {
 253     // TODO Auto-generated method stub
 254     return "";
 255   }
 256 }