package jalview.ws.slivkaws;
import jalview.bin.Cache;
-import jalview.gui.AlignFrame;
+import jalview.ws.ServiceChangeListener;
import jalview.ws.WSDiscovererI;
import jalview.ws.api.ServiceWithParameters;
-import jalview.ws.jws2.PreferredServiceRegistry;
-
-import java.beans.PropertyChangeListener;
-import java.beans.PropertyChangeSupport;
import java.io.IOException;
import java.net.MalformedURLException;
-import java.net.URISyntaxException;
import java.net.URL;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.List;
-
-import javax.swing.JMenu;
-
+import java.util.Set;
+import java.util.Vector;
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.CopyOnWriteArraySet;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+
+import compbio.data.msa.Category;
import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
{
private static final String SLIVKA_HOST_URLS = "SLIVKAHOSTURLS";
- private static final String COMPBIO_SLIVKA = "https://www.compbio.dundee.ac.uk/slivka";
+ private static final String COMPBIO_SLIVKA = "https://www.compbio.dundee.ac.uk/slivka/";
private static SlivkaWSDiscoverer instance = null;
return instance;
}
- private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
- this);
+ private Set<ServiceChangeListener> serviceListeners = new CopyOnWriteArraySet<>();
@Override
- public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
+ public void addServiceChangeListener(ServiceChangeListener l)
{
- JMenu slivkaMenu = new JMenu("Slivka");
- wsmenu.add(slivkaMenu);
-
- 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);
-
+ serviceListeners.add(l);
}
- volatile boolean ready = false;
-
- volatile Thread discovererThread = null;
-
- private class DiscovererThread extends Thread
+ @Override
+ public void removeServiceChangeListener(ServiceChangeListener l)
{
- private Thread oldThread;
-
- DiscovererThread(Thread oldThread)
- {
- super();
- this.oldThread = oldThread;
- }
+ serviceListeners.remove(l);
+ }
- @Override
- public void run()
+ public void notifyServiceListeners(List<ServiceWithParameters> services)
+ {
+ for (var listener : serviceListeners)
{
- if (oldThread != null)
- {
- oldThread.interrupt();
- try
- {
- oldThread.join();
- } catch (InterruptedException e)
- {
- return;
- } finally
- {
- oldThread = null;
- }
- }
- ready = false;
- reloadServices();
- ready = !isInterrupted();
+ listener.servicesChanged(this, services);
}
}
- Thread discoverer = null;
+ private final ExecutorService executor = Executors
+ .newSingleThreadExecutor();
- @Override
- public Thread startDiscoverer(PropertyChangeListener changeListener)
+ private Vector<Future<?>> discoveryTasks = new Vector<>();
+
+ public CompletableFuture<WSDiscovererI> startDiscoverer()
{
- changeSupport.addPropertyChangeListener(changeListener);
- ready = false;
- (discovererThread = new DiscovererThread(discovererThread)).start();
- return discovererThread;
+ CompletableFuture<WSDiscovererI> task = CompletableFuture
+ .supplyAsync(() -> {
+ reloadServices();
+ return SlivkaWSDiscoverer.this;
+ }, executor);
+ discoveryTasks.add(task);
+ return task;
}
- private void reloadServices()
+ private List<ServiceWithParameters> reloadServices()
{
Cache.log.info("Reloading Slivka services");
- changeSupport.firePropertyChange("services", services, List.of());
+ notifyServiceListeners(Collections.emptyList());
ArrayList<ServiceWithParameters> instances = new ArrayList<>();
for (String url : getServiceUrls())
{
- Cache.log.info(url);
- SlivkaClient client;
+ SlivkaClient client = new SlivkaClient(url);
+
+ List<SlivkaService> services;
try
{
- client = new SlivkaClient(url);
- } catch (URISyntaxException e)
+ services = client.getServices();
+ } catch (IOException e)
{
e.printStackTrace();
continue;
}
- try
+ for (SlivkaService service : services)
{
- for (SlivkaService service : client.getServices())
+ SlivkaWSInstance newInstance = null;
+ for (String classifier : service.classifiers)
{
- SlivkaWSInstance newinstance = null;
- for (String classifier : service.classifiers)
+ String[] path = classifier.split("\\s*::\\s*");
+ if (path.length >= 3 && path[0].toLowerCase().equals("operation")
+ && path[1].toLowerCase().equals("analysis"))
{
- if (classifier.contains("Multiple sequence alignment"))
- {
- newinstance = new SlivkaMsaServiceInstance(client, service);
- }
- if (classifier.contains("Protein sequence analysis")
- && newinstance == null)
+ switch (path[path.length - 1].toLowerCase())
{
- newinstance = new SlivkaAnnotationServiceInstance(client,
- service, false);
+ case "sequence alignment analysis (conservation)":
+ newInstance = new SlivkaAnnotationServiceInstance(client,
+ service, Category.CATEGORY_CONSERVATION);
+ break;
+ case "protein sequence analysis":
+ newInstance = new SlivkaAnnotationServiceInstance(client,
+ service, Category.CATEGORY_DISORDER);
+ break;
+ case "protein secondary structure prediction":
+ newInstance = new SlivkaAnnotationServiceInstance(client,
+ service, "Secondary Structure Prediction");
+ break;
+ case "multiple sequence alignment":
+ newInstance = new SlivkaMsaServiceInstance(client, service,
+ Category.CATEGORY_ALIGNMENT);
+ break;
}
- if (classifier
- .contains("Sequence alignment analysis (conservation)"))
- {
- newinstance = new SlivkaAnnotationServiceInstance(client,
- service, true);
- }
- }
- if (newinstance != null)
- {
- instances.add(newinstance);
}
+ if (newInstance != null)
+ break;
}
- } catch (IOException e)
- {
- continue;
+ if (newInstance != null)
+ instances.add(newInstance);
}
}
services = instances;
- changeSupport.firePropertyChange("services", List.of(), services);
-
Cache.log.info("Slivka services reloading finished");
+ notifyServiceListeners(instances);
+ return instances;
}
@Override
@Override
public boolean hasServices()
{
- return ready == true && services.size() > 0;
+ return !isRunning() && services.size() > 0;
}
@Override
public boolean isRunning()
{
- return discovererThread == null || discovererThread.isAlive()
- || discovererThread.getState() == Thread.State.NEW;
+ return !discoveryTasks.stream().allMatch(Future::isDone);
}
@Override
} catch (MalformedURLException e)
{
Cache.log.warn("Problem whilst trying to make a URL from '"
- + ((url != null) ? url : "<null>") + "'");
+ + ((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)");
+ "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);
}
}
{
List<?> services = new SlivkaClient(url).getServices();
return services.isEmpty() ? STATUS_NO_SERVICES : STATUS_OK;
- } catch (IOException | URISyntaxException e)
+ } catch (IOException | org.json.JSONException e)
{
+ Cache.log.error("Slivka could not retrieve services list", e);
return STATUS_INVALID;
}
}
git://source.jalview.org / jalview.git / blobdiff