X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=afeb53a0434ee4d7f80c2dc5fbfd4548d8bee81f;hb=0bfc20cd41e038f203443ffd1245d469fdb95c68;hp=9b4c008af388f248bc782bc4867ad7eaecdff6e0;hpb=f149a335b5467a4802eded5da0ca2fc732d7caf7;p=jalview.git diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index 9b4c008..afeb53a 100644 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -22,7 +22,6 @@ import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; -import java.io.Closeable; import java.net.ConnectException; import java.net.URL; import java.util.ArrayList; @@ -45,14 +44,12 @@ import jalview.gui.AlignFrame; import jalview.gui.Desktop; import jalview.gui.JalviewChangeSupport; import jalview.gui.JvSwingUtils; +import jalview.util.jarInputStreamProvider; import jalview.ws.WSMenuEntryProviderI; -import jalview.ws.jws2.Jws2Discoverer.Jws2Instance; -import jalview.ws.params.ParamDatastoreI; -import compbio.data.msa.MsaWS; +import jalview.ws.jws2.jabaws2.Jws2Instance; +import compbio.data.msa.JABAService; import compbio.metadata.Option; import compbio.metadata.Preset; -import compbio.metadata.PresetManager; -import compbio.metadata.RunnerConfig; import compbio.ws.client.Jws2Client; import compbio.ws.client.Services; @@ -136,6 +133,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI Cache.log.debug("Old discovery thread has finished."); } running = true; + changeSupport.firePropertyChange("services", services, new Vector()); oldthread = Thread.currentThread(); try { @@ -162,17 +160,28 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { invalidServiceUrls.removeAllElements(); } + ArrayList svctypes=new ArrayList(); List qrys = new ArrayList(); for (final String jwsservers : getServiceUrls()) { JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsservers); + if (svctypes.size()==0) + { + // TODO: remove this ugly hack to get Canonical JABA service ordering for all possible services + for (Services sv:squery.JABAWS2SERVERS) + { + svctypes.add(sv.toString()); + } + + } qrys.add(squery); new Thread(squery).start(); } - boolean finished = false; + boolean finished = true; do { + finished=true; try { Thread.sleep(100); @@ -182,7 +191,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI ; for (JabaWsServerQuery squery : qrys) { - finished |= !squery.isRunning(); + finished = finished && !squery.isRunning(); } if (aborted) { @@ -194,12 +203,32 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } } } while (!aborted && !finished); - oldthread = null; - running = false; if (!aborted) { - changeSupport.firePropertyChange("services", new Vector(), services); + // resort services according to order found in jabaws service list + // also ensure servics for each host are ordered in same way. + + if (services!=null && services.size()>0) + { + Jws2Instance[] svcs=new Jws2Instance[services.size()]; + int[] spos=new int[services.size()]; + int ipos=0; + Vector svcUrls = getServiceUrls(); + for (Jws2Instance svc:services) + { + svcs[ipos]=svc; + spos[ipos++]=1000*svcUrls.indexOf(svc.getHost()) + 1+svctypes.indexOf(svc.serviceType); + } + jalview.util.QuickSort.sort(spos, svcs); + services=new Vector(); + for (Jws2Instance svc:svcs) { + services.add(svc); + } + } } + oldthread = null; + running = false; + changeSupport.firePropertyChange("services", new Vector(), services); } /** @@ -209,17 +238,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI * @param srv * @param service2 */ - synchronized void addService(String jwsservers, Services srv, - MsaWS service2) + synchronized void addService(String jwsservers, Jws2Instance service) { if (services == null) { services = new Vector(); } System.out.println("Discovered service: " + jwsservers + " " - + srv.toString()); - Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(), - service2); + + service.toString()); +// Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(), +// service2); services.add(service); // retrieve the presets and parameter set and cache now @@ -227,188 +255,27 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI service.hasParameters(); } - public class Jws2Instance - { - public String hosturl; - - public String serviceType; - - public MsaWS service; - - public Jws2Instance(String hosturl, String serviceType, MsaWS service) - { - super(); - this.hosturl = hosturl; - this.serviceType = serviceType; - this.service = service; - } - - PresetManager presets = null; - - public JabaParamStore paramStore = null; - - /** - * non thread safe - gets the presets for this service (blocks whilst it - * calls the service to get the preset set) - * - * @return service presets or null if exceptions were raised. - */ - public PresetManager getPresets() - { - if (presets == null) - { - try - { - presets = service.getPresets(); - } catch (Exception ex) - { - System.err - .println("Exception when retrieving presets for service " - + serviceType + " at " + hosturl); - } - } - return presets; - } - - public String getHost() - { - return hosturl; - /* - * try { URL serviceurl = new URL(hosturl); if (serviceurl.getPort()!=80) - * { return serviceurl.getHost()+":"+serviceurl.getPort(); } return - * serviceurl.getHost(); } catch (Exception e) { - * System.err.println("Failed to parse service URL '" + hosturl + - * "' as a valid URL!"); } return null; - */ - } - - /** - * @return short description of what the service will do - */ - public String getActionText() - { - return "Align with " + serviceType; - } - - /** - * non-thread safe - blocks whilst accessing service to get complete set of - * available options and parameters - * - * @return - */ - public RunnerConfig getRunnerConfig() - { - return service.getRunnerOptions(); - } - - @Override - protected void finalize() throws Throwable - { - if (service != null) - { - try - { - Closeable svc = (Closeable) service; - service = null; - svc.close(); - } catch (Exception e) - { - } - ; - } - super.finalize(); - } - - public ParamDatastoreI getParamStore() - { - if (paramStore == null) - { - try - { - paramStore = new JabaParamStore(this, - (Desktop.instance != null ? Desktop - .getUserParameterStore() : null)); - } catch (Exception ex) - { - } - - } - return paramStore; - } - - public String getUri() - { - // this is only valid for Jaba 1.0 - this formula might have to change! - return hosturl - + (hosturl.lastIndexOf("/") == (hosturl.length() - 1) ? "" - : "/") + serviceType; - } - - private boolean hasParams = false, lookedForParams = false; - - public boolean hasParameters() - { - if (!lookedForParams) - { - lookedForParams = true; - try - { - hasParams = (getRunnerConfig().getArguments().size() > 0); - } catch (Exception e) - { - - } - } - return hasParams; - } - }; - /** * holds list of services. */ protected Vector services; - + /** + * attach all available web services to the appropriate submenu in the given JMenu + */ public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame) { // dynamically regenerate service list. - final JMenu jws2al = wsmenu; // new JMenu("JABAWS Alignment"); - jws2al.addMenuListener(new MenuListener() - { - // TODO: future: add menu listener to parent menu - so submenus are - // populated *before* they are selected. - @Override - public void menuSelected(MenuEvent e) - { - populateWSMenuEntry(jws2al, alignFrame); - } - - @Override - public void menuDeselected(MenuEvent e) - { - // TODO Auto-generated method stub - - } - - @Override - public void menuCanceled(MenuEvent e) - { - // TODO Auto-generated method stub - - } - - }); - wsmenu.add(jws2al); - + populateWSMenuEntry(wsmenu, alignFrame, null); } - private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame) + private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame, String typeFilter) { if (running || services == null || services.size() == 0) { return; } - boolean byhost = Cache.getDefault("WSMENU_BYHOST", true), bytype = Cache - .getDefault("WSMENU_BYTYPE", true); + boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache + .getDefault("WSMENU_BYTYPE", false); /** * eventually, JWS2 services will appear under the same align/etc submenus. * for moment we keep them separate. @@ -417,9 +284,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI MsaWSClient msacl = new MsaWSClient(); Vector hostLabels = new Vector(); jws2al.removeAll(); - String lasthost = null; + Hashtable lasthostFor = new Hashtable(); Hashtable> hosts = new Hashtable>(); - String[] sorton; + ArrayList hostlist=new ArrayList(); for (Jws2Instance service : services) { ArrayList hostservices = hosts.get(service.getHost()); @@ -427,12 +294,11 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { hosts.put(service.getHost(), hostservices = new ArrayList()); + hostlist.add(service.getHost()); } hostservices.add(service); } - sorton = hosts.keySet().toArray(new String[1]); - String hostlist[] = sorton.clone(); - jalview.util.QuickSort.sort(sorton, hostlist); + // now add hosts in order of the given array for (String host : hostlist) { Jws2Instance orderedsvcs[] = hosts.get(host).toArray( @@ -445,7 +311,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI jalview.util.QuickSort.sort(sortbytype, orderedsvcs); for (final Jws2Instance service : orderedsvcs) { - atpoint = jws2al; + atpoint = JvSwingUtils.findOrCreateMenu(jws2al,service.action); String type = service.serviceType; if (byhost) { @@ -475,7 +341,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI // group JMenuItem hitm; atpoint.addSeparator(); - if (lasthost == null || !lasthost.equals(host)) + if (lasthostFor.get(service.action) == null || !lasthostFor.get(service.action).equals(host)) { atpoint.add(hitm = new JMenuItem(host)); hitm.setForeground(Color.blue); @@ -490,14 +356,15 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI }); hitm.setToolTipText(JvSwingUtils .wrapTooltip("Opens the JABAWS server's homepage in web browser")); - lasthost = host; + lasthostFor.put(service.action,host); } hostLabels.addElement(host + service.serviceType + service.getActionText()); // hostLabels.addElement(host + (bytype ? // service.serviceType+service.getActionText() : "")); } - msacl.attachWSMenuEntry(atpoint, service, alignFrame); + + service.attachWSMenuEntry(atpoint, alignFrame); /* * JMenuItem sitem = new JMenuItem(service.serviceType); * sitem.setToolTipText("Hosted at " + service.hosturl); @@ -517,6 +384,14 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI public static void main(String[] args) { + if (args.length>0) + { + testUrls = new Vector(); + for (String url:args) + { + testUrls.add(url); + }; + } Thread runner = getDiscoverer().startDiscoverer( new PropertyChangeListener() { @@ -527,6 +402,11 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { System.out.println("Changesupport: There are now " + getDiscoverer().services.size() + " services"); + int i=1; + for (Jws2Instance instance:getDiscoverer().services) + { + System.out.println("Service "+i+++" "+instance.getClass()+"@"+instance.getHost()+": "+instance.getActionText()); + } } } @@ -541,6 +421,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } ; } + try { + Thread.sleep(50); + } catch (InterruptedException x) {} } private static Jws2Discoverer discoverer; @@ -590,8 +473,14 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } } + private static Vector testUrls=null; public static Vector getServiceUrls() { + if (testUrls!=null) + { + // return test urls, if there are any, instead of touching cache + return testUrls; + } String surls = Cache.getDefault(JWS2HOSTURLS, "http://www.compbio.dundee.ac.uk/jabaws"); Vector urls = new Vector(); @@ -800,5 +689,4 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } return null; } - }