X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=afeb53a0434ee4d7f80c2dc5fbfd4548d8bee81f;hb=0bfc20cd41e038f203443ffd1245d469fdb95c68;hp=5bce82fcc3346506682bddcf7e59ac21b1ea39c3;hpb=c19a31fdb3569eb58b03a5dacf14ae0102bd2caa;p=jalview.git diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index 5bce82f..afeb53a 100644 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@ -1,27 +1,57 @@ +/* + * 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. + * + * 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.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.util.jarInputStreamProvider; import jalview.ws.WSMenuEntryProviderI; -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.ws.client.Jws2Base; -import compbio.ws.client.Jws2Base.Services; +import compbio.ws.client.Jws2Client; +import compbio.ws.client.Services; /** * discoverer for jws2 services. Follows the lightweight service discoverer @@ -59,74 +89,144 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI changeSupport.removePropertyChangeListener(listener); } - boolean running = false; + 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; - @Override public void run() { - if (running) + if (running && oldthread != null && oldthread.isAlive()) { - return; + if (!aborted) + { + return; + } + while (running) + { + try + { + Cache.log + .debug("Waiting around for old discovery thread to finish."); + // wait around until old discoverer dies + Thread.sleep(100); + } catch (Exception e) + { + } + } + Cache.log.debug("Old discovery thread has finished."); } running = true; + changeSupport.firePropertyChange("services", services, new Vector()); + oldthread = Thread.currentThread(); try { Class foo = getClass().getClassLoader().loadClass( - "compbio.ws.client.JwsBase"); + "compbio.ws.client.Jws2Client"); } catch (ClassNotFoundException e) { System.err - .println("Not enabling Jalview Webservices version 2: client jar is not available." - +"\nPlease check that your webstart JNLP file is up to date!"); + .println("Not enabling JABA Webservices : client jar is not available." + + "\nPlease check that your webstart JNLP file is up to date!"); running = false; return; } - // 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 + // reinitialise records of good and bad service URLs + if (services != null) + { + services.removeAllElements(); + } + if (urlsWithoutServices != null) + { + urlsWithoutServices.removeAllElements(); + } + if (invalidServiceUrls != null) + { + invalidServiceUrls.removeAllElements(); + } + ArrayList svctypes=new ArrayList(); + + List qrys = new ArrayList(); + for (final String jwsservers : getServiceUrls()) { - if (Jws2Base.validURL(jwsservers)) + JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsservers); + if (svctypes.size()==0) { - // look for services - for (Services srv : Jws2Base.Services.values()) + // TODO: remove this ugly hack to get Canonical JABA service ordering for all possible services + for (Services sv:squery.JABAWS2SERVERS) { - MsaWS service = null; - try - { - service = Jws2Base.connect(jwsservers, srv); - } catch (Exception e) - { - System.err.println("Jws2 Discoverer: Problem with " - + jwsservers + " with service " + srv + ":\n" - + e.getMessage()); - if (!(e instanceof javax.xml.ws.WebServiceException)) - { - e.printStackTrace(); - } - } - ; - if (service != null) - { - addService(jwsservers, srv, service); - } + svctypes.add(sv.toString()); } } - else + qrys.add(squery); + new Thread(squery).start(); + } + boolean finished = true; + do + { + finished=true; + try + { + Thread.sleep(100); + } catch (Exception e) { - Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers); } - } catch (Exception e) - { - e.printStackTrace(); - Cache.log.warn("Exception when discovering Jws2 services.", e); - } catch (Error e) + ; + for (JabaWsServerQuery squery : qrys) + { + finished = finished && !squery.isRunning(); + } + if (aborted) + { + Cache.log.debug("Aborting " + qrys.size() + + " JABAWS discovery threads."); + for (JabaWsServerQuery squery : qrys) + { + squery.setQuit(true); + } + } + } while (!aborted && !finished); + if (!aborted) { - Cache.log.error("Exception when discovering Jws2 services.", e); + // 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); } @@ -138,114 +238,179 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI * @param srv * @param service2 */ - private 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()); - services.add(new Jws2Instance(jwsservers, "Align with " - + srv.toString(), service2)); - } - - public class Jws2Instance - { - String hosturl; + + service.toString()); +// Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(), +// service2); - String serviceType; - - MsaWS service; - - public Jws2Instance(String hosturl, String serviceType, MsaWS service) - { - super(); - this.hosturl = hosturl; - this.serviceType = serviceType; - this.service = service; - } - - PresetManager presets = 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; - } - }; + services.add(service); + // retrieve the presets and parameter set and cache now + service.getParamStore().getPresets(); + service.hasParameters(); + } /** * holds list of services. */ - Vector services; - - @Override + 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. + populateWSMenuEntry(wsmenu, alignFrame, null); + } + + private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame, String typeFilter) + { 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) - { - msacl.attachWSMenuEntry(jws2, 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); } }); - */ + Vector hostLabels = new Vector(); + jws2al.removeAll(); + Hashtable lasthostFor = new Hashtable(); + Hashtable> hosts = new Hashtable>(); + ArrayList hostlist=new ArrayList(); + for (Jws2Instance service : services) + { + ArrayList hostservices = hosts.get(service.getHost()); + if (hostservices == null) + { + hosts.put(service.getHost(), + hostservices = new ArrayList()); + hostlist.add(service.getHost()); + } + hostservices.add(service); } - if (services.size() > 0) + // now add hosts in order of the given array + 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 = JvSwingUtils.findOrCreateMenu(jws2al,service.action); + 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 (lasthostFor.get(service.action) == null || !lasthostFor.get(service.action).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")); + lasthostFor.put(service.action,host); + } + hostLabels.addElement(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) { - Thread runner = new Thread(getDiscoverer()); - getDiscoverer().addPropertyChangeListener(new PropertyChangeListener() + if (args.length>0) { - - @Override - public void propertyChange(PropertyChangeEvent evt) + testUrls = new Vector(); + for (String url:args) { - System.out.println("Changesupport: There are now " - + getDiscoverer().services.size() + " services"); - } - }); - runner.start(); + testUrls.add(url); + }; + } + 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"); + int i=1; + for (Jws2Instance instance:getDiscoverer().services) + { + System.out.println("Service "+i+++" "+instance.getClass()+"@"+instance.getHost()+": "+instance.getActionText()); + } + + } + } + }); while (runner.isAlive()) { try @@ -256,6 +421,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } ; } + try { + Thread.sleep(50); + } catch (InterruptedException x) {} } private static Jws2Discoverer discoverer; @@ -280,4 +448,245 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI 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); + } + } + + 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(); + 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; + } }