package jalview.ws.slivkaws;
-import jalview.gui.AlignFrame;
-import jalview.ws.WSMenuEntryProviderI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.ws.ServiceChangeListener;
+import jalview.ws.WSDiscovererI;
import jalview.ws.api.ServiceWithParameters;
-import jalview.ws.jws2.PreferredServiceRegistry;
+import javajs.http.HttpClientFactory;
-import java.beans.PropertyChangeSupport;
-import java.io.IOError;
import java.io.IOException;
-import java.net.URISyntaxException;
+import java.net.MalformedURLException;
+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;
-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 slivkaClient;
+ private List<ServiceWithParameters> services = List.of();
private SlivkaWSDiscoverer()
{
- try
- {
- slivkaClient = new SlivkaClient("localhost", 4954);
- } catch (URISyntaxException e)
- {
- throw new RuntimeException(e);
- }
}
public static SlivkaWSDiscoverer getInstance()
return instance;
}
- List<ServiceWithParameters> getServiceInstances()
+ private Set<ServiceChangeListener> serviceListeners = new CopyOnWriteArraySet<>();
+
+ @Override
+ public void addServiceChangeListener(ServiceChangeListener l)
+ {
+ serviceListeners.add(l);
+ }
+
+ @Override
+ public void removeServiceChangeListener(ServiceChangeListener l)
+ {
+ serviceListeners.remove(l);
+ }
+
+ public void notifyServiceListeners(List<ServiceWithParameters> services)
{
- List<ServiceWithParameters> instances = new ArrayList<>();
- for (SlivkaService service : services)
+ for (var listener : serviceListeners)
{
- for (String classifier : service.classifiers)
+ listener.servicesChanged(this, services);
+ }
+ }
+
+ private final ExecutorService executor = Executors
+ .newSingleThreadExecutor();
+
+ private Vector<Future<?>> discoveryTasks = new Vector<>();
+
+ public CompletableFuture<WSDiscovererI> startDiscoverer()
+ {
+ CompletableFuture<WSDiscovererI> task = CompletableFuture
+ .supplyAsync(() -> {
+ reloadServices();
+ return SlivkaWSDiscoverer.this;
+ }, executor);
+ discoveryTasks.add(task);
+ return task;
+ }
+
+ private List<ServiceWithParameters> reloadServices()
+ {
+ Console.info("Reloading Slivka services");
+ notifyServiceListeners(Collections.emptyList());
+ ArrayList<ServiceWithParameters> instances = new ArrayList<>();
+
+ for (String url : getServiceUrls())
+ {
+ SlivkaClient client = new SlivkaClient(url);
+
+ List<SlivkaService> services;
+ try
{
- if (classifier.contains("Multiple sequence alignment"))
- {
- instances
- .add(new SlivkaMsaServiceInstance(slivkaClient, service));
- }
- else if (classifier.contains("Protein sequence analysis"))
- {
- instances.add(new SlivkaAnnotationServiceInstance(slivkaClient,
- service, false));
- }
- else if (classifier
- .contains("Sequence alignment analysis (conservation)"))
+ services = client.getServices();
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ continue;
+ }
+ for (SlivkaService service : services)
+ {
+ SlivkaWSInstance newInstance = null;
+ for (String classifier : service.classifiers)
{
- instances.add(new SlivkaAnnotationServiceInstance(slivkaClient,
- service, true));
+ String[] path = classifier.split("\\s*::\\s*");
+ if (path.length >= 3 && path[0].toLowerCase().equals("operation")
+ && path[1].toLowerCase().equals("analysis"))
+ {
+ switch (path[path.length - 1].toLowerCase())
+ {
+ case "rna secondary structure prediction":
+ newInstance = new RNAalifoldServiceInstance(client,
+ service, "Secondary Structure Prediction");
+ break;
+ 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 (newInstance != null)
+ break;
}
-
+ if (newInstance != null)
+ instances.add(newInstance);
}
}
+
+ services = instances;
+ Console.info("Slivka services reloading finished");
+ notifyServiceListeners(instances);
return instances;
}
- private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
- this);
-
@Override
- public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
+ public List<ServiceWithParameters> getServices()
{
- 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(
- getServiceInstances(),
- changeSupport, slivkaMenu, alignFrame, null);
-
+ return services;
}
- List<SlivkaService>services=null;
+ @Override
+ public boolean hasServices()
+ {
+ return !isRunning() && services.size() > 0;
+ }
- volatile boolean started = false, finished = false;
+ @Override
+ public boolean isRunning()
+ {
+ return !discoveryTasks.stream().allMatch(Future::isDone);
+ }
- Thread discoverer = null;
@Override
- public void run()
+ public void setServiceUrls(List<String> wsUrls)
{
- discoverer = Thread.currentThread();
- started = true;
- try
+ if (wsUrls != null && !wsUrls.isEmpty())
{
- services = slivkaClient.getServices();
- } catch (IOException e)
+ Cache.setProperty(SLIVKA_HOST_URLS, String.join(",", wsUrls));
+ }
+ else
{
- throw new IOError(e);
+ Cache.removeProperty(SLIVKA_HOST_URLS);
}
- finished = true;
}
- public static List<ServiceWithParameters> getServices()
+ @Override
+ public List<String> getServiceUrls()
{
- SlivkaWSDiscoverer us = getInstance();
- if (us.services == null)
+ String surls = Cache.getDefault(SLIVKA_HOST_URLS, COMPBIO_SLIVKA);
+ String[] urls = surls.split(",");
+ ArrayList<String> valid = new ArrayList<>(urls.length);
+ for (String url : urls)
{
- us.run();
+ try
+ {
+ new URL(url);
+ valid.add(url);
+ } catch (MalformedURLException e)
+ {
+ Console.warn("Problem whilst trying to make a URL from '"
+ + ((url != null) ? url : "<null>") + "'");
+ Console.warn(
+ "This was probably due to a malformed comma separated list"
+ + " in the " + SLIVKA_HOST_URLS
+ + " entry of $(HOME)/.jalview_properties)");
+ Console.debug("Exception was ", e);
+ }
}
- return us.getServiceInstances();
+ return valid;
}
- public boolean hasServices()
+ @Override
+ public boolean testServiceUrl(URL url)
{
- return finished == true && services != null && services.size() > 0;
+ return getServerStatusFor(url.toString()) == STATUS_OK;
}
- public boolean isRunning()
+ @Override
+ public int getServerStatusFor(String url)
+ {
+ try
+ {
+ List<?> services = new SlivkaClient(url).getServices();
+ return services.isEmpty() ? STATUS_NO_SERVICES : STATUS_OK;
+ } catch (IOException | org.json.JSONException e)
+ {
+ Console.error("Slivka could not retrieve services list", e);
+ return STATUS_INVALID;
+ }
+ }
+
+ @Override
+ public String getErrorMessages()
{
- return discoverer != null && discoverer.isAlive();
+ // TODO Auto-generated method stub
+ return "";
}
}
git://source.jalview.org / jalview.git / blobdiff