X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=8e298178006e16b8baa47f800ab1dd76af783aed;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=6aa4607b10a40a87ff1686750862b0ef0bdd5cce;hpb=3bf633c1b8b4a7a3ea6cf12f7df675a77c9ae4b6;p=jalview.git diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index 6aa4607..8e29817 100644 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@ -1,27 +1,55 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 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.HashSet; +import java.util.Hashtable; +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.ws.WSMenuEntryProviderI; +import jalview.ws.params.ParamDatastoreI; import compbio.data.msa.MsaWS; +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.metadata.RunnerConfig; +import compbio.ws.client.Jws2Client; +import compbio.ws.client.Services; /** * discoverer for jws2 services. Follows the lightweight service discoverer @@ -61,72 +89,77 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI boolean running = false; - @Override + Thread oldthread = null; + public void run() { - if (running) + if (running && oldthread != null && oldthread.isAlive()) { return; } running = true; + oldthread = Thread.currentThread(); try { Class foo = getClass().getClassLoader().loadClass( - "compbio.ws.client.Jws2Base"); + "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!"); + + "\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 + if (services != null) + { + services.removeAllElements(); + } + for (String jwsservers : getServiceUrls()) { - if (Jws2Base.validURL(jwsservers)) + try { - // look for services - for (Services srv : Jws2Base.Services.values()) + if (Jws2Client.validURL(jwsservers)) { - MsaWS service = null; - try - { - service = Jws2Base.connect(jwsservers, srv); - } catch (Exception e) + // look for services + for (Services srv : Services.values()) { - System.err.println("Jws2 Discoverer: Problem with " - + jwsservers + " with service " + srv + ":\n" - + e.getMessage()); - if (!(e instanceof javax.xml.ws.WebServiceException)) + MsaWS service = null; + try { - e.printStackTrace(); + service = Jws2Client.connect(jwsservers, srv); + } catch (Exception e) + { + System.err.println("Jws2 Discoverer: Problem on " + + jwsservers + " with service " + srv + ":\n" + + e.getMessage()); + if (!(e instanceof javax.xml.ws.WebServiceException)) + { + e.printStackTrace(); + } + } + ; + if (service != null) + { + addService(jwsservers, srv, service); } } - ; - if (service != null) - { - addService(jwsservers, srv, service); - } - } - } - else + } + else + { + 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) { - Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers); + Cache.log.error("Exception when discovering Jws2 services.", e); } - } catch (Exception e) - { - e.printStackTrace(); - Cache.log.warn("Exception when discovering Jws2 services.", e); - } catch (Error e) - { - Cache.log.error("Exception when discovering Jws2 services.", e); } + oldthread = null; running = false; changeSupport.firePropertyChange("services", new Vector(), services); } @@ -146,17 +179,21 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } System.out.println("Discovered service: " + jwsservers + " " + srv.toString()); - services.add(new Jws2Instance(jwsservers, "Align with " - + 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(); + 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) { @@ -168,6 +205,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI 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) @@ -190,29 +229,219 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } 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; + + /** + * find or add a submenu with the given title in the given menu + * + * @param menu + * @param submenu + * @return the new or existing submenu + */ + private JMenu findOrCreateMenu(JMenu menu, String submenu) + { + JMenu submenuinstance = null; + for (int i = 0, iSize = menu.getMenuComponentCount(); i < iSize; i++) + { + if (menu.getMenuComponent(i) instanceof JMenu + && ((JMenu) menu.getMenuComponent(i)).getText().equals( + submenu)) + { + submenuinstance = (JMenu) menu.getMenuComponent(i); + } + } + if (submenuinstance == null) + { + submenuinstance = new JMenu(submenu); + menu.add(submenuinstance); + } + return submenuinstance; + + } - @Override public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame) { + // dynamically regenerate service list. + final JMenu jws2al = 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", true), bytype = Cache + .getDefault("WSMENU_BYTYPE", true); /** * 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(); + Vector hostLabels = new Vector(); + jws2al.removeAll(); + String lasthost=null; for (final Jws2Instance service : services) { - msacl.attachWSMenuEntry(jws2, service, alignFrame); + atpoint = jws2al; + String host = service.getHost(); + String type = service.serviceType; + if (byhost) + { + atpoint = findOrCreateMenu(atpoint, host); + if (atpoint.getToolTipText() == null) + { + atpoint.setToolTipText("Services at " + host); + } + } + if (bytype) + { + atpoint = 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); + 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); @@ -225,11 +454,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI * alignFrame); } }); */ } - if (services.size() > 0) - { - wsmenu.add(jws2); - } - } public static void main(String[] args) @@ -238,7 +462,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI getDiscoverer().addPropertyChangeListener(new PropertyChangeListener() { - @Override public void propertyChange(PropertyChangeEvent evt) { System.out.println("Changesupport: There are now " @@ -280,4 +503,109 @@ 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); + } + } + + 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) + { + return false; + } catch (OutOfMemoryError e) + { + return false; + } catch (Error e) + { + return false; + } + return true; + } + }