X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fslivkaws%2FSlivkaWSDiscoverer.java;h=d21d5d1f85c6d4e96f57c22d42d09135e5afc2e6;hb=ab58313e7bb31264ddb2715a1c548cdc789d7fa6;hp=993d8ed8ea89f2e9d2c4330ec5083baaae4144b2;hpb=6e6734420cf5c85cc4d2b0b2730142b0dd8431a5;p=jalview.git diff --git a/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java b/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java index 993d8ed8..d21d5d1 100644 --- a/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java +++ b/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java @@ -1,34 +1,42 @@ package jalview.ws.slivkaws; -import jalview.gui.AlignFrame; -import jalview.ws.WSMenuEntryProviderI; -import jalview.ws.jws2.MsaWSClient; -import jalview.ws.jws2.SequenceAnnotationWSClient; +import jalview.bin.Cache; +import jalview.bin.Console; +import jalview.ws.ServiceChangeListener; +import jalview.ws.WSDiscovererI; +import jalview.ws.api.ServiceWithParameters; +import javajs.http.HttpClientFactory; -import java.io.IOError; import java.io.IOException; -import java.net.URISyntaxException; - -import javax.swing.JMenu; - +import java.net.MalformedURLException; +import java.net.URL; +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; +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 services = List.of(); private SlivkaWSDiscoverer() { - try - { - slivkaClient = new SlivkaClient("gjb-www-1.cluster.lifesci.dundee.ac.uk", 3203); - } catch (URISyntaxException e) - { - throw new RuntimeException(e); - } } public static SlivkaWSDiscoverer getInstance() @@ -40,80 +48,191 @@ public class SlivkaWSDiscoverer implements Runnable, WSMenuEntryProviderI return instance; } - private void addMsaServiceClient(JMenu alignmentMenu, - SlivkaService service, AlignFrame alignFrame) + private Set serviceListeners = new CopyOnWriteArraySet<>(); + + @Override + public void addServiceChangeListener(ServiceChangeListener l) { - SlivkaMsaServiceInstance instance = new SlivkaMsaServiceInstance( - slivkaClient, service); - MsaWSClient client = new MsaWSClient(); - client.attachWSMenuEntry(alignmentMenu, instance, alignFrame); - alignmentMenu.addSeparator(); + serviceListeners.add(l); } - private void addDisorderServiceClient(JMenu disorderMenu, - SlivkaService service, AlignFrame alignFrame) + @Override + public void removeServiceChangeListener(ServiceChangeListener l) { - SlivkaAnnotationServiceInstance serviceInstance = new SlivkaAnnotationServiceInstance( - slivkaClient, service, false); - SequenceAnnotationWSClient client = new SequenceAnnotationWSClient(); - client.attachWSMenuEntry(disorderMenu, serviceInstance, alignFrame); - disorderMenu.addSeparator(); + serviceListeners.remove(l); } - private void addConservationServiceClient(JMenu conservationMenu, - SlivkaService service, AlignFrame alignFrame) + public void notifyServiceListeners(List services) { - SlivkaAnnotationServiceInstance serviceInstance = new SlivkaAnnotationServiceInstance( - slivkaClient, service, true); - SequenceAnnotationWSClient client = new SequenceAnnotationWSClient(); - client.attachWSMenuEntry(conservationMenu, serviceInstance, alignFrame); - conservationMenu.addSeparator(); + for (var listener : serviceListeners) + { + listener.servicesChanged(this, services); + } } - @Override - public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame) + private final ExecutorService executor = Executors + .newSingleThreadExecutor(); + + private Vector> discoveryTasks = new Vector<>(); + + public CompletableFuture startDiscoverer() { - 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); - try + CompletableFuture task = CompletableFuture + .supplyAsync(() -> { + reloadServices(); + return SlivkaWSDiscoverer.this; + }, executor); + discoveryTasks.add(task); + return task; + } + + private List reloadServices() + { + Console.info("Reloading Slivka services"); + notifyServiceListeners(Collections.emptyList()); + ArrayList instances = new ArrayList<>(); + + for (String url : getServiceUrls()) { - for (SlivkaService service : slivkaClient.getServices()) + SlivkaClient client = new SlivkaClient(url); + + List services; + try + { + services = client.getServices(); + } catch (IOException e) { + e.printStackTrace(); + continue; + } + for (SlivkaService service : services) + { + SlivkaWSInstance newInstance = null; for (String classifier : service.classifiers) { - if (classifier.contains("Multiple sequence alignment")) - { - addMsaServiceClient(alignmentMenu, service, alignFrame); - } - else if (classifier.contains("Protein sequence analysis")) + String[] path = classifier.split("\\s*::\\s*"); + if (path.length >= 3 && path[0].toLowerCase().equals("operation") + && path[1].toLowerCase().equals("analysis")) { - addDisorderServiceClient(disorderMenu, service, alignFrame); + 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; + } } - else if (classifier - .contains("Sequence alignment analysis (conservation)")) - { - addConservationServiceClient(conservationMenu, service, - alignFrame); - } - + if (newInstance != null) + break; } + if (newInstance != null) + instances.add(newInstance); } - } catch (IOException e) + } + + services = instances; + Console.info("Slivka services reloading finished"); + notifyServiceListeners(instances); + return instances; + } + + @Override + public List getServices() + { + return services; + } + + @Override + public boolean hasServices() + { + return !isRunning() && services.size() > 0; + } + + @Override + public boolean isRunning() + { + return !discoveryTasks.stream().allMatch(Future::isDone); + } + + @Override + public void setServiceUrls(List wsUrls) + { + if (wsUrls != null && !wsUrls.isEmpty()) { - throw new IOError(e); + Cache.setProperty(SLIVKA_HOST_URLS, String.join(",", wsUrls)); + } + else + { + Cache.removeProperty(SLIVKA_HOST_URLS); } } @Override - public void run() + public List getServiceUrls() { + String surls = Cache.getDefault(SLIVKA_HOST_URLS, COMPBIO_SLIVKA); + String[] urls = surls.split(","); + ArrayList valid = new ArrayList<>(urls.length); + for (String url : urls) + { + try + { + new URL(url); + valid.add(url); + } catch (MalformedURLException e) + { + Console.warn("Problem whilst trying to make a URL from '" + + ((url != null) ? url : "") + "'"); + 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; + } + @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 | org.json.JSONException e) + { + Console.error("Slivka could not retrieve services list", e); + return STATUS_INVALID; + } + } + + @Override + public String getErrorMessages() + { + // TODO Auto-generated method stub + return ""; } }