X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=ed808f6e03a5022f501c5e9879beec63994a1bc8;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=2d8eaa6e9e1559c609a2ec6b5141d359b41c07a6;hpb=b793de8470fd1824f60169477a00cc3282f58907;p=jalview.git diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index 2d8eaa6..ed808f6 100644 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@ -1,22 +1,60 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, 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 + * 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 . + */ package jalview.ws.jws2; +import java.awt.Color; 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; import java.util.HashSet; +import java.util.Hashtable; +import java.util.List; +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.Jws2Discoverer.Jws2Instance; +import jalview.ws.params.ParamDatastoreI; import compbio.data.msa.MsaWS; -import compbio.ws.client.Jws2Base; -import compbio.ws.client.Jws2Base.Services; +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; /** * discoverer for jws2 services. Follows the lightweight service discoverer @@ -27,56 +65,141 @@ import compbio.ws.client.Jws2Base.Services; */ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { - compbio.data.msa.MsaWS service; - boolean running=false; - @Override + private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( + this); + + /** + * change listeners are notified of "services" property changes + * + * @param listener + * to be added that consumes new services Hashtable object. + */ + public void addPropertyChangeListener( + java.beans.PropertyChangeListener listener) + { + changeSupport.addPropertyChangeListener(listener); + } + + /** + * + * + * @param listener + * to be removed + */ + public void removePropertyChangeListener( + java.beans.PropertyChangeListener listener) + { + changeSupport.removePropertyChangeListener(listener); + } + + boolean running = false, aborted = false; + + /** + * @return the aborted + */ + public boolean isAborted() + { + return aborted; + } + + /** + * @param aborted + * the aborted to set + */ + public void setAborted(boolean aborted) + { + this.aborted = aborted; + } + + Thread oldthread = null; + public void run() { - if (running) + if (running && oldthread != null && oldthread.isAlive()) { - return; - } - running=true; -// Cache.initLogger(); -// Cache.log.setLevel(Level.DEBUG); - // TODO: Document and PACK JWS2 - String jwsservers = Cache.getDefault("JWS2HOSTURLS", - "http://webservices.compbio.dundee.ac.uk:8084/jws2"); - try - { - if (Jws2Base.validURL(jwsservers)) + if (!aborted) + { + return; + } + while (running) { - // look for services - for (Services srv : Jws2Base.Services.values()) + try + { + Cache.log + .debug("Waiting around for old discovery thread to finish."); + // wait around until old discoverer dies + Thread.sleep(100); + } catch (Exception e) { - MsaWS service = null; - try - { - service = Jws2Base.connect(jwsservers, srv); - } catch (Exception e) - { - } - ; - if (service != null) - { - addService(jwsservers, srv, service); - } } + } + Cache.log.debug("Old discovery thread has finished."); + } + running = true; + oldthread = Thread.currentThread(); + try + { + Class foo = getClass().getClassLoader().loadClass( + "compbio.ws.client.Jws2Client"); + } catch (ClassNotFoundException e) + { + System.err + .println("Not enabling JABA Webservices : client jar is not available." + + "\nPlease check that your webstart JNLP file is up to date!"); + running = false; + return; + } + // reinitialise records of good and bad service URLs + if (services != null) + { + services.removeAllElements(); + } + if (urlsWithoutServices != null) + { + urlsWithoutServices.removeAllElements(); + } + if (invalidServiceUrls != null) + { + invalidServiceUrls.removeAllElements(); + } + List qrys = new ArrayList(); + for (final String jwsservers : getServiceUrls()) + { + JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsservers); + qrys.add(squery); + new Thread(squery).start(); + } + boolean finished = false; + do + { + try + { + Thread.sleep(100); + } catch (Exception e) + { } - else + ; + for (JabaWsServerQuery squery : qrys) { - Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers); + finished |= !squery.isRunning(); } - } catch (Exception e) - { - Cache.log.warn("Exception when discovering Jws2 services.", e); - } catch (Error e) + if (aborted) + { + Cache.log.debug("Aborting " + qrys.size() + + " JABAWS discovery threads."); + for (JabaWsServerQuery squery : qrys) + { + squery.setQuit(true); + } + } + } while (!aborted && !finished); + oldthread = null; + running = false; + if (!aborted) { - Cache.log.error("Exception when discovering Jws2 services.", e); + changeSupport.firePropertyChange("services", new Vector(), services); } - running=false; - } /** @@ -86,24 +209,31 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI * @param srv * @param service2 */ - private void addService(String jwsservers, Services srv, MsaWS service2) + synchronized void addService(String jwsservers, Services srv, + MsaWS service2) { - Cache.log.info("Discovered service: " + jwsservers + " " - + srv.toString()); - if (services==null) { + if (services == null) + { services = new Vector(); } - services.add(new Jws2Instance(jwsservers, "Align with " - + srv.toString(), service2)); + System.out.println("Discovered service: " + jwsservers + " " + + srv.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(); } public class Jws2Instance { - String hosturl; + public String hosturl; - String serviceType; + public String serviceType; - MsaWS service; + public MsaWS service; public Jws2Instance(String hosturl, String serviceType, MsaWS service) { @@ -113,55 +243,294 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI 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. */ - Vector services; + protected Vector services; - @Override public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame) { - if (running || services==null || services.size() == 0) + // 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); + + } + + private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame) + { + if (running || services == null || services.size() == 0) { 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 jws2 = new JMenu("JWS2 Alignment"); + JMenu atpoint; MsaWSClient msacl = new MsaWSClient(); - for (final Jws2Instance service : services) + Vector hostLabels = new Vector(); + jws2al.removeAll(); + String lasthost = null; + Hashtable> hosts = new Hashtable>(); + String[] sorton; + for (Jws2Instance service : services) { - msacl.attachWSMenuEntry(jws2, service, alignFrame); - /*JMenuItem sitem = new JMenuItem(service.serviceType); - sitem.setToolTipText("Hosted at " + service.hosturl); - sitem.addActionListener(new ActionListener() + ArrayList hostservices = hosts.get(service.getHost()); + if (hostservices == null) { - - @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); - } - });*/ + hosts.put(service.getHost(), + hostservices = new ArrayList()); + } + hostservices.add(service); } - if (services.size()>0) + sorton = hosts.keySet().toArray(new String[1]); + String hostlist[] = sorton.clone(); + jalview.util.QuickSort.sort(sorton, hostlist); + for (String host : hostlist) { - wsmenu.add(jws2); + Jws2Instance orderedsvcs[] = hosts.get(host).toArray( + new Jws2Instance[1]); + String sortbytype[] = new String[orderedsvcs.length]; + for (int i = 0; i < sortbytype.length; i++) + { + sortbytype[i] = orderedsvcs[i].serviceType; + } + jalview.util.QuickSort.sort(sortbytype, orderedsvcs); + for (final Jws2Instance service : orderedsvcs) + { + atpoint = jws2al; + String type = service.serviceType; + if (byhost) + { + atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host); + if (atpoint.getToolTipText() == null) + { + atpoint.setToolTipText("Services at " + host); + } + } + if (bytype) + { + atpoint = JvSwingUtils.findOrCreateMenu(atpoint, type); + if (atpoint.getToolTipText() == null) + { + atpoint.setToolTipText(service.getActionText()); + } + } + if (!byhost + && !hostLabels.contains(host + service.serviceType + + service.getActionText())) + // !hostLabels.contains(host + (bytype ? + // service.serviceType+service.getActionText() : ""))) + { + // add a marker indicating where this service is hosted + // relies on services from the same host being listed in a + // contiguous + // group + JMenuItem hitm; + atpoint.addSeparator(); + if (lasthost == null || !lasthost.equals(host)) + { + atpoint.add(hitm = new JMenuItem(host)); + 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")); + lasthost = host; + } + hostLabels.addElement(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); } + * }); + */ + } } - + } + public static void main(String[] args) { - Thread runner = new Thread(getDiscoverer()); - runner.start(); + Thread runner = getDiscoverer().startDiscoverer( + new PropertyChangeListener() + { + + public void propertyChange(PropertyChangeEvent evt) + { + if (getDiscoverer().services != null) + { + System.out.println("Changesupport: There are now " + + getDiscoverer().services.size() + " services"); + + } + } + }); while (runner.isAlive()) { try @@ -173,10 +542,12 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI ; } } + private static Jws2Discoverer discoverer; + public static Jws2Discoverer getDiscoverer() { - if (discoverer==null) + if (discoverer == null) { discoverer = new Jws2Discoverer(); } @@ -186,7 +557,248 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI public boolean hasServices() { // TODO Auto-generated method stub - return services!=null && services.size()>0; + return !running && services != null && services.size() > 0; + } + + public boolean isRunning() + { + return running; + } + + /** + * the jalview .properties entry for JWS2 URLS + */ + final static String JWS2HOSTURLS = "JWS2HOSTURLS"; + + public static void setServiceUrls(Vector urls) + { + if (urls != null) + { + StringBuffer urlbuffer = new StringBuffer(); + String sep = ""; + for (String url : urls) + { + urlbuffer.append(sep); + urlbuffer.append(url); + sep = ","; + } + Cache.setProperty(JWS2HOSTURLS, urlbuffer.toString()); + } + else + { + Cache.removeProperty(JWS2HOSTURLS); + } + } + + public static Vector getServiceUrls() + { + String surls = Cache.getDefault(JWS2HOSTURLS, + "http://www.compbio.dundee.ac.uk/jabaws"); + Vector urls = new Vector(); + try + { + StringTokenizer st = new StringTokenizer(surls, ","); + while (st.hasMoreElements()) + { + String url = null; + try + { + java.net.URL u = new java.net.URL(url = st.nextToken()); + if (!urls.contains(url)) + { + urls.add(url); + } + else + { + jalview.bin.Cache.log.info("Ignoring duplicate url in " + + JWS2HOSTURLS + " list"); + } + } catch (Exception ex) + { + jalview.bin.Cache.log + .warn("Problem whilst trying to make a URL from '" + + ((url != null) ? url : "") + "'"); + jalview.bin.Cache.log + .warn("This was probably due to a malformed comma separated list" + + " in the " + + JWS2HOSTURLS + + " entry of $(HOME)/.jalview_properties)"); + jalview.bin.Cache.log.debug("Exception was ", ex); + } + } + } catch (Exception ex) + { + jalview.bin.Cache.log.warn( + "Error parsing comma separated list of urls in " + + JWS2HOSTURLS + " preference.", ex); + } + if (urls.size() >= 0) + { + return urls; + } + return null; + } + + public Vector getServices() + { + return (services == null) ? new Vector() + : new Vector(services); + } + + /** + * test the given URL with the JabaWS test code + * + * @param foo + * @return + */ + public static boolean testServiceUrl(URL foo) + { + try + { + compbio.ws.client.WSTester.main(new String[] + { "-h=" + foo.toString() }); + } catch (Exception e) + { + e.printStackTrace(); + return false; + } catch (OutOfMemoryError e) + { + e.printStackTrace(); + return false; + } catch (Error e) + { + e.printStackTrace(); + return false; + } + + return true; + } + + /** + * Start a fresh discovery thread and notify the given object when we're + * finished. Any known existing threads will be killed before this one is + * started. + * + * @param changeSupport2 + * @return new thread + */ + public Thread startDiscoverer(PropertyChangeListener changeSupport2) + { + if (isRunning()) + { + setAborted(true); + } + addPropertyChangeListener(changeSupport2); + Thread thr = new Thread(this); + thr.start(); + return thr; + } + + Vector invalidServiceUrls = null, urlsWithoutServices = null; + + /** + * @return the invalidServiceUrls + */ + public Vector getInvalidServiceUrls() + { + return invalidServiceUrls; + } + + /** + * @return the urlsWithoutServices + */ + public Vector getUrlsWithoutServices() + { + return urlsWithoutServices; + } + + /** + * add an 'empty' JABA server to the list. Only servers not already in the + * 'bad URL' list will be added to this list. + * + * @param jwsservers + */ + public synchronized void addUrlwithnoservices(String jwsservers) + { + if (urlsWithoutServices == null) + { + urlsWithoutServices = new Vector(); + } + + if ((invalidServiceUrls == null || !invalidServiceUrls + .contains(jwsservers)) + && !urlsWithoutServices.contains(jwsservers)) + { + urlsWithoutServices.add(jwsservers); + } + } + + /** + * add a bad URL to the list + * + * @param jwsservers + */ + public synchronized void addInvalidServiceUrl(String jwsservers) + { + if (invalidServiceUrls == null) + { + invalidServiceUrls = new Vector(); + } + if (!invalidServiceUrls.contains(jwsservers)) + { + invalidServiceUrls.add(jwsservers); + } + } + + /** + * + * @return a human readable report of any problems with the service URLs used + * for discovery + */ + public String getErrorMessages() + { + if (!isRunning() && !isAborted()) + { + StringBuffer ermsg = new StringBuffer(); + boolean list = false; + if (getInvalidServiceUrls() != null + && getInvalidServiceUrls().size() > 0) + { + ermsg.append("URLs that could not be contacted: \n"); + for (String svcurl : getInvalidServiceUrls()) + { + if (list) + { + ermsg.append(", "); + } + list = true; + ermsg.append(svcurl); + } + ermsg.append("\n\n"); + } + list = false; + if (getUrlsWithoutServices() != null + && getUrlsWithoutServices().size() > 0) + { + ermsg.append("URLs without any JABA Services : \n"); + for (String svcurl : getUrlsWithoutServices()) + { + if (list) + { + ermsg.append(", "); + } + list = true; + ermsg.append(svcurl); + } + ermsg.append("\n"); + } + if (ermsg.length() > 1) + { + return ermsg.toString(); + } + + } + return null; } - + }