X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=c0addfe15af47c67839584f56e5d4558c7574cbe;hb=23a5ed32b702d4d3682b8cdc8fd8e3f238202f7d;hp=8907b581a93b513708a9e3b6e633c18a46b187a9;hpb=8c2e72fec911f86333cbc82aaed4d29fadac542c;p=jalview.git diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index 8907b58..c0addfe 100644 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@ -17,39 +17,32 @@ */ package jalview.ws.jws2; +import jalview.bin.Cache; +import jalview.gui.AlignFrame; +import jalview.gui.Desktop; +import jalview.gui.JvSwingUtils; +import jalview.ws.WSMenuEntryProviderI; +import jalview.ws.jws2.jabaws2.Jws2Instance; + import java.awt.Color; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; -import java.net.ConnectException; import java.net.URL; import java.util.ArrayList; +import java.util.Arrays; +import java.util.HashMap; import java.util.HashSet; import java.util.Hashtable; import java.util.List; +import java.util.Map; import java.util.StringTokenizer; import java.util.Vector; import javax.swing.JMenu; import javax.swing.JMenuItem; -import javax.swing.event.MenuEvent; -import javax.swing.event.MenuListener; -import org.apache.log4j.Level; - -import jalview.bin.Cache; -import jalview.datamodel.AlignmentView; -import jalview.gui.AlignFrame; -import jalview.gui.Desktop; -import jalview.gui.JalviewChangeSupport; -import jalview.gui.JvSwingUtils; -import jalview.ws.WSMenuEntryProviderI; -import jalview.ws.jws2.jabaws2.Jws2Instance; -import compbio.data.msa.JABAService; -import compbio.metadata.Option; -import compbio.metadata.Preset; -import compbio.ws.client.Jws2Client; import compbio.ws.client.Services; /** @@ -132,6 +125,7 @@ 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 { @@ -158,17 +152,32 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { invalidServiceUrls.removeAllElements(); } + if (validServiceUrls != null) + { + validServiceUrls.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); @@ -178,7 +187,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI ; for (JabaWsServerQuery squery : qrys) { - finished |= !squery.isRunning(); + finished = finished && !squery.isRunning(); } if (aborted) { @@ -190,12 +199,32 @@ 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); } /** @@ -205,68 +234,167 @@ 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 service.getParamStore().getPresets(); service.hasParameters(); + if (validServiceUrls==null) + { + validServiceUrls=new Vector(); + } + validServiceUrls.add(jwsservers); } /** * 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() + populateWSMenuEntry(wsmenu, alignFrame, null); + } + private boolean isRecalculable(String action) { + return (action!=null && action.equalsIgnoreCase("conservation")); + } + private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame, String typeFilter) + { + if (running || services == null || services.size() == 0) { - // 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); + return; + } + 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. + */ + JMenu atpoint; + List enumerableServices=new ArrayList(); + //jws2al.removeAll(); + Map preferredHosts=new HashMap(); + Map> alternates = new HashMap>(); + for (Jws2Instance service : services.toArray(new Jws2Instance[0])) + { + if (!isRecalculable(service.action)) { + // add 'one shot' services to be displayed using the classic menu structure + enumerableServices.add(service); + } else { + if (!preferredHosts.containsKey(service.serviceType)) + { + Jws2Instance preferredInstance = getPreferredServiceFor(alignFrame, + service.serviceType); + if (preferredInstance != null) + { + preferredHosts.put(service.serviceType, preferredInstance); + } + else + { + preferredHosts.put(service.serviceType, service); + } + } + List ph=alternates.get(service.serviceType); + if (preferredHosts.get(service.serviceType)!=service) + { + if (ph==null) + { + ph=new ArrayList(); + } + ph.add(service); + alternates.put(service.serviceType, ph); + } } - @Override - public void menuDeselected(MenuEvent e) - { - // TODO Auto-generated method stub + } + // create GUI element for classic services + addEnumeratedServices(jws2al, alignFrame, enumerableServices); + // and the instantaneous services + for (final Jws2Instance service : preferredHosts.values()) + { + atpoint = JvSwingUtils.findOrCreateMenu(jws2al,service.action); + JMenuItem hitm; + if (atpoint.getItemCount()>1) { + // previous service of this type already present + atpoint.addSeparator(); } - - @Override - public void menuCanceled(MenuEvent e) + atpoint.add(hitm = new JMenuItem(service.getHost())); + hitm.setForeground(Color.blue); + hitm.addActionListener(new ActionListener() { - // TODO Auto-generated method stub - } + @Override + public void actionPerformed(ActionEvent e) + { + Desktop.showUrl(service.getHost()); + } + }); + hitm.setToolTipText(JvSwingUtils + .wrapTooltip("Opens the JABAWS server's homepage in web browser")); + + service.attachWSMenuEntry(atpoint, alignFrame); + if (alternates.containsKey(service.serviceType)) + { + atpoint.add(hitm=new JMenu("Switch server")); + hitm.setToolTipText(JvSwingUtils.wrapTooltip("Choose a server for running this service")); + for (final Jws2Instance sv:alternates.get(service.serviceType)) + { + JMenuItem itm; + hitm.add(itm=new JMenuItem(sv.getHost())); + itm.setForeground(Color.blue); + itm.addActionListener(new ActionListener() + { - }); - wsmenu.add(jws2al); + @Override + public void actionPerformed(ActionEvent arg0) + { + new Thread(new Runnable() { + public void run() { + setPreferredServiceFor(alignFrame, sv.serviceType, sv.action, sv); + changeSupport.firePropertyChange("services", new Vector(), services); + }; + }).start(); + + } + }); + } + /*hitm.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent arg0) + { + new Thread(new Runnable() { + @Override + public void run() + { + new SetPreferredServer(alignFrame, service.serviceType, service.action); + } + }).start(); + } + });*/ + } + } } - - private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame) + /** + * add services using the Java 2.5/2.6/2.7 system which optionally creates submenus to index by host and service program type + */ + private void addEnumeratedServices(final JMenu jws2al, final AlignFrame alignFrame, List enumerableServices) { - if (running || services == null || services.size() == 0) - { - return; - } boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache .getDefault("WSMENU_BYTYPE", false); /** @@ -275,24 +403,22 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI */ JMenu atpoint; MsaWSClient msacl = new MsaWSClient(); - Vector hostLabels = new Vector(); - jws2al.removeAll(); - String lasthost = null; + List hostLabels = new ArrayList(); + Hashtable lasthostFor = new Hashtable(); Hashtable> hosts = new Hashtable>(); - String[] sorton; - for (Jws2Instance service : services) + ArrayList hostlist=new ArrayList(); + for (Jws2Instance service : enumerableServices) { ArrayList hostservices = hosts.get(service.getHost()); if (hostservices == null) { 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( @@ -305,7 +431,7 @@ 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) { @@ -334,8 +460,12 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI // contiguous // group JMenuItem hitm; - atpoint.addSeparator(); - if (lasthost == null || !lasthost.equals(host)) + if (hostLabels.contains(host)) { + atpoint.addSeparator(); + } else { + hostLabels.add(host); + } + if (lasthostFor.get(service.action) == null || !lasthostFor.get(service.action).equals(host)) { atpoint.add(hitm = new JMenuItem(host)); hitm.setForeground(Color.blue); @@ -350,33 +480,26 @@ 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 + hostLabels.add(host + service.serviceType + service.getActionText()); - // hostLabels.addElement(host + (bytype ? - // service.serviceType+service.getActionText() : "")); } - msacl.attachWSMenuEntry(atpoint, service, alignFrame); - /* - * JMenuItem sitem = new JMenuItem(service.serviceType); - * sitem.setToolTipText("Hosted at " + service.hosturl); - * sitem.addActionListener(new ActionListener() { - * - * @Override public void actionPerformed(ActionEvent e) { AlignmentView - * msa = alignFrame.gatherSequencesForAlignment(); MsaWSClient client = - * new MsaWSClient(service, "JWS2 Alignment of " + - * alignFrame.getTitle(), msa, false, true, - * alignFrame.getViewport().getAlignment().getDataset(), alignFrame); } - * }); - */ + + service.attachWSMenuEntry(atpoint, alignFrame); } } - } - 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() { @@ -387,6 +510,11 @@ 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()); + } } } @@ -401,6 +529,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } ; } + try { + Thread.sleep(50); + } catch (InterruptedException x) {} } private static Jws2Discoverer discoverer; @@ -450,8 +581,14 @@ 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(); @@ -554,7 +691,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI return thr; } - Vector invalidServiceUrls = null, urlsWithoutServices = null; + Vector invalidServiceUrls = null, urlsWithoutServices = null, validServiceUrls=null; /** * @return the invalidServiceUrls @@ -661,4 +798,114 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI return null; } + public int getServerStatusFor(String url) + { + if (validServiceUrls!=null && validServiceUrls.contains(url)) + { + return 1; + } + if (urlsWithoutServices!=null && urlsWithoutServices.contains(url)) + return 0; + if (invalidServiceUrls!=null && invalidServiceUrls.contains(url)) + { + return -1; + } + return -2; + } + + /** + * pick the user's preferred service based on a set of URLs (jaba server locations) and service URIs (specifying version and service interface class) + * + * @param serviceURL + * @return null or best match for given uri/ls. + */ + public Jws2Instance getPreferredServiceFor(String[] serviceURLs) + { + HashSet urls=new HashSet(); + urls.addAll(Arrays.asList(serviceURLs)); + Jws2Instance match=null; + for (Jws2Instance svc:services) + { + if (urls.contains(svc.getServiceTypeURI())) + { + if (match==null) { + // for moment we always pick service from server ordered first in user's preferences + match=svc; + } + if (urls.contains(svc.getUri())) + { + // stop and return - we've matched type URI and URI for service endpoint + return svc; + } + } + } + return match; + } + + Map> preferredServiceMap = new HashMap>(); +; + + /** + * get current preferred service of the given type, or global default + * @param af null or a specific alignFrame + * @param serviceType Jws2Instance.serviceType for service + * @return null if no service of this type is available, the preferred service for the serviceType and af if specified and if defined. + */ + public Jws2Instance getPreferredServiceFor(AlignFrame af, + String serviceType) + { + String serviceurl = null; + synchronized (preferredServiceMap) + { + String afid = (af == null) ? "" : af.getViewport().getSequenceSetId(); + Map prefmap = preferredServiceMap.get(afid); + if (afid.length() > 0 && prefmap == null) + { + // recover global setting, if any + prefmap = preferredServiceMap.get(""); + } + if (prefmap != null) + { + serviceurl = prefmap.get(serviceType); + } + + } + Jws2Instance response = null; + for (Jws2Instance svc : services) + { + if (svc.serviceType.equals(serviceType)) + { + if (serviceurl == null || serviceurl.equals(svc.getHost())) + { + response = svc; + break; + } + } + } + return response; + } + + public void setPreferredServiceFor(AlignFrame af, String serviceType, + String serviceAction, Jws2Instance selectedServer) + { + String afid = (af == null) ? "" : af.getViewport().getSequenceSetId(); + if (preferredServiceMap == null) + { + preferredServiceMap = new HashMap>(); + } + Map prefmap = preferredServiceMap.get(afid); + if (prefmap == null) + { + prefmap = new HashMap(); + preferredServiceMap.put(afid, prefmap); + } + prefmap.put(serviceType, selectedServer.getHost()); + prefmap.put(serviceAction, selectedServer.getHost()); + } + + public void setPreferredServiceFor(String serviceType, + String serviceAction, Jws2Instance selectedServer) + { + setPreferredServiceFor(null, serviceType, serviceAction, selectedServer); + } }