X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=99a17269ede8f82eeb1b0cf05d0478bbc5e5c3a4;hb=8364d3900ad4271d460ae15a245add45c66c2e89;hp=b6e74934592b874bb1a1e0cf420b0dfc2cf1e84f;hpb=888625c12e9f320a2763de770401fda5964d5de4;p=jalview.git diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index b6e7493..99a1726 100644 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@ -1,13 +1,13 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR @@ -32,9 +32,11 @@ import java.beans.PropertyChangeListener; 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; @@ -154,16 +156,17 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { validServiceUrls.removeAllElements(); } - ArrayList svctypes=new ArrayList(); + ArrayList svctypes = new ArrayList(); List qrys = new ArrayList(); for (final String jwsservers : getServiceUrls()) { JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsservers); - if (svctypes.size()==0) + if (svctypes.size() == 0) { - // TODO: remove this ugly hack to get Canonical JABA service ordering for all possible services - for (Services sv:squery.JABAWS2SERVERS) + // TODO: remove this ugly hack to get Canonical JABA service ordering + // for all possible services + for (Services sv : squery.JABAWS2SERVERS) { svctypes.add(sv.toString()); } @@ -175,7 +178,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI boolean finished = true; do { - finished=true; + finished = true; try { Thread.sleep(100); @@ -201,21 +204,23 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { // 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) + + if (services != null && services.size() > 0) { - Jws2Instance[] svcs=new Jws2Instance[services.size()]; - int[] spos=new int[services.size()]; - int ipos=0; + Jws2Instance[] svcs = new Jws2Instance[services.size()]; + int[] spos = new int[services.size()]; + int ipos = 0; Vector svcUrls = getServiceUrls(); - for (Jws2Instance svc:services) + for (Jws2Instance svc : services) { - svcs[ipos]=svc; - spos[ipos++]=1000*svcUrls.indexOf(svc.getHost()) + 1+svctypes.indexOf(svc.serviceType); + 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 = new Vector(); + for (Jws2Instance svc : svcs) + { services.add(svc); } } @@ -240,16 +245,20 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } System.out.println("Discovered service: " + jwsservers + " " + service.toString()); -// Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(), -// service2); + // Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(), + // service2); services.add(service); // retrieve the presets and parameter set and cache now - service.getParamStore().getPresets(); + ParamDataStoreI pds = service.getParamStore(); + if (pds != null) + { + pds.getPresets(); + } service.hasParameters(); - if (validServiceUrls==null) + if (validServiceUrls == null) { - validServiceUrls=new Vector(); + validServiceUrls = new Vector(); } validServiceUrls.add(jwsservers); } @@ -258,8 +267,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI * holds list of services. */ protected Vector services; + /** - * attach all available web services to the appropriate submenu in the given JMenu + * attach all available web services to the appropriate submenu in the given + * JMenu */ public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame) { @@ -267,7 +278,13 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI populateWSMenuEntry(wsmenu, alignFrame, null); } - private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame, String typeFilter) + 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) { @@ -280,13 +297,137 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI * 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); + } + } + + } + + // 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(); + } + atpoint.add(hitm = new JMenuItem(service.getHost())); + hitm.setForeground(Color.blue); + hitm.addActionListener(new ActionListener() + { + + @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() + { + + @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(); } }); + */ + } + } + } + + /** + * 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) + { + 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; MsaWSClient msacl = new MsaWSClient(); - Vector hostLabels = new Vector(); - jws2al.removeAll(); - Hashtable lasthostFor = new Hashtable(); + List hostLabels = new ArrayList(); + Hashtable lasthostFor = new Hashtable(); Hashtable> hosts = new Hashtable>(); - ArrayList hostlist=new ArrayList(); - for (Jws2Instance service : services) + ArrayList hostlist = new ArrayList(); + for (Jws2Instance service : enumerableServices) { ArrayList hostservices = hosts.get(service.getHost()); if (hostservices == null) @@ -310,7 +451,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI jalview.util.QuickSort.sort(sortbytype, orderedsvcs); for (final Jws2Instance service : orderedsvcs) { - atpoint = JvSwingUtils.findOrCreateMenu(jws2al,service.action); + atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action); String type = service.serviceType; if (byhost) { @@ -339,8 +480,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI // contiguous // group JMenuItem hitm; - atpoint.addSeparator(); - if (lasthostFor.get(service.action) == null || !lasthostFor.get(service.action).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); @@ -355,41 +504,27 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI }); hitm.setToolTipText(JvSwingUtils .wrapTooltip("Opens the JABAWS server's homepage in web browser")); - lasthostFor.put(service.action,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() : "")); } - + service.attachWSMenuEntry(atpoint, 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); } - * }); - */ } } - } public static void main(String[] args) { - if (args.length>0) + if (args.length > 0) { testUrls = new Vector(); - for (String url:args) + for (String url : args) { testUrls.add(url); - }; + } + ; } Thread runner = getDiscoverer().startDiscoverer( new PropertyChangeListener() @@ -401,10 +536,13 @@ 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) + int i = 1; + for (Jws2Instance instance : getDiscoverer().services) { - System.out.println("Service "+i+++" "+instance.getClass()+"@"+instance.getHost()+": "+instance.getActionText()); + System.out.println("Service " + i++ + " " + + instance.getClass() + "@" + + instance.getHost() + ": " + + instance.getActionText()); } } @@ -420,9 +558,12 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } ; } - try { + try + { Thread.sleep(50); - } catch (InterruptedException x) {} + } catch (InterruptedException x) + { + } } private static Jws2Discoverer discoverer; @@ -472,10 +613,11 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } } - private static Vector testUrls=null; + private static Vector testUrls = null; + public static Vector getServiceUrls() { - if (testUrls!=null) + if (testUrls != null) { // return test urls, if there are any, instead of touching cache return testUrls; @@ -582,7 +724,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI return thr; } - Vector invalidServiceUrls = null, urlsWithoutServices = null, validServiceUrls=null; + Vector invalidServiceUrls = null, urlsWithoutServices = null, + validServiceUrls = null; /** * @return the invalidServiceUrls @@ -691,13 +834,13 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI public int getServerStatusFor(String url) { - if (validServiceUrls!=null && validServiceUrls.contains(url)) + if (validServiceUrls != null && validServiceUrls.contains(url)) { return 1; } - if (urlsWithoutServices!=null && urlsWithoutServices.contains(url)) - return 0; - if (invalidServiceUrls!=null && invalidServiceUrls.contains(url)) + if (urlsWithoutServices != null && urlsWithoutServices.contains(url)) + return 0; + if (invalidServiceUrls != null && invalidServiceUrls.contains(url)) { return -1; } @@ -705,31 +848,109 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } /** - * pick the user's preferred service based on a set of URLs (jaba server locations) and service URIs (specifying version and service interface class) + * 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(); + HashSet urls = new HashSet(); urls.addAll(Arrays.asList(serviceURLs)); - Jws2Instance match=null; - for (Jws2Instance svc:services) + Jws2Instance match = null; + if (services != null) { - if (urls.contains(svc.getServiceTypeURI())) + for (Jws2Instance svc : services) { - if (match==null) { - // for moment we always pick service from server ordered first in user's preferences - match=svc; - } - if (urls.contains(svc.getUri())) + if (urls.contains(svc.getServiceTypeURI())) { - // stop and return - we've matched type URI and URI for service endpoint - return svc; + 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); + } }