package jalview.ws.slivkaws;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.ws.ServiceChangeListener;
import jalview.ws.WSDiscovererI;
import jalview.ws.api.ServiceWithParameters;
-import java.beans.PropertyChangeListener;
+import javajs.http.HttpClientFactory;
+
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;
-import java.util.concurrent.FutureTask;
+import compbio.data.msa.Category;
import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
}
}
- private final ExecutorService executor = Executors.newSingleThreadExecutor();
+ private final ExecutorService executor = Executors
+ .newSingleThreadExecutor();
+
private Vector<Future<?>> discoveryTasks = new Vector<>();
public CompletableFuture<WSDiscovererI> startDiscoverer()
private List<ServiceWithParameters> reloadServices()
{
- Cache.log.info("Reloading Slivka services");
+ Console.info("Reloading Slivka services");
notifyServiceListeners(Collections.emptyList());
ArrayList<ServiceWithParameters> instances = new ArrayList<>();
for (String url : getServiceUrls())
{
- Cache.log.info(url);
- SlivkaClient client;
- client = new SlivkaClient(url);
+ SlivkaClient client = new SlivkaClient(url);
+
+ List<SlivkaService> services;
try
{
- for (SlivkaService service : client.getServices())
+ services = client.getServices();
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ continue;
+ }
+ for (SlivkaService service : services)
+ {
+ 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"))
+ switch (path[path.length - 1].toLowerCase())
{
- newinstance = new SlivkaMsaServiceInstance(client, service);
+ 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 (classifier.contains("Protein sequence analysis")
- && newinstance == null)
- {
- newinstance = new SlivkaAnnotationServiceInstance(client,
- service, false);
- }
- 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)
- {
- e.printStackTrace();
- continue;
+ if (newInstance != null)
+ instances.add(newInstance);
}
}
services = instances;
+ Console.info("Slivka services reloading finished");
notifyServiceListeners(instances);
- Cache.log.info("Slivka services reloading finished");
return instances;
}
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);
+ 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 valid;
{
List<?> services = new SlivkaClient(url).getServices();
return services.isEmpty() ? STATUS_NO_SERVICES : STATUS_OK;
- } catch (IOException e)
+ } catch (IOException | org.json.JSONException e)
{
- Cache.log.error("Slivka could not retrieve services list", e);
+ Console.error("Slivka could not retrieve services list", e);
return STATUS_INVALID;
}
}