X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=0782d57dba94f575044570955770a7de87bcf303;hb=2f4f1d8fb6878271b64f327bc58c895f458137af;hp=1c912d89f3f1be41ec5376ff33be88fd75aa8756;hpb=52a6409c5880b3e108e7c77e756222ed22f6b87f;p=jalview.git diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index 1c912d8..0782d57 100644 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@ -1,55 +1,51 @@ /* - * 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 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors * * 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 * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ 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 jalview.ws.params.ParamDatastoreI; + 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.Set; 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; /** @@ -111,6 +107,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI public void run() { + if (running && oldthread != null && oldthread.isAlive()) { if (!aborted) @@ -132,6 +129,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI Cache.log.debug("Old discovery thread has finished."); } running = true; + + // first set up exclusion list if needed + final Set ignoredServices = new HashSet(); + for (String ignored:jalview.bin.Cache.getDefault("IGNORED_JABAWS_SERVICETYPES", Services.JpredWS.toString()).split("\\|")) + { + ignoredServices.add(ignored); + } + + + changeSupport.firePropertyChange("services", services, new Vector()); oldthread = Thread.currentThread(); try { @@ -158,17 +165,36 @@ 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) + { + if (!ignoredServices.contains(sv.toString())) + { + 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 +204,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI ; for (JabaWsServerQuery squery : qrys) { - finished |= !squery.isRunning(); + if (squery.isRunning()){ + finished=false; + } } if (aborted) { @@ -190,12 +218,37 @@ 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) + { + if (!ignoredServices.contains(svc.serviceType)) + { + services.add(svc); + } + } + } } + oldthread = null; + running = false; + changeSupport.firePropertyChange("services", new Vector(), services); } /** @@ -213,21 +266,32 @@ 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) + { + 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 + * attach all available web services to the appropriate submenu in the given + * JMenu */ public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame) { @@ -235,7 +299,13 @@ 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) { @@ -248,25 +318,148 @@ 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(); - 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( @@ -279,7 +472,7 @@ 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) { @@ -308,8 +501,16 @@ 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); @@ -324,41 +525,27 @@ 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() : "")); } - + 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() @@ -370,6 +557,14 @@ 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()); + } } } @@ -384,6 +579,12 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } ; } + try + { + Thread.sleep(50); + } catch (InterruptedException x) + { + } } private static Jws2Discoverer discoverer; @@ -433,10 +634,11 @@ 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; @@ -543,7 +745,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI return thr; } - Vector invalidServiceUrls = null, urlsWithoutServices = null; + Vector invalidServiceUrls = null, urlsWithoutServices = null, + validServiceUrls = null; /** * @return the invalidServiceUrls @@ -649,4 +852,126 @@ 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; + if (services != 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); + } }