/* * Jalview - A Sequence Alignment Editor and Viewer * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program 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 2 * of the License, or (at your option) any later version. * * This program 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 this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ package jalview.ws; /** *

Title:

* *

Description:

* *

Copyright: Copyright (c) 2004

* *

Company: Dundee University

* * @author not attributable * @version 1.0 */ import ext.vamsas.*; import java.util.Vector; import java.util.Hashtable; import java.util.StringTokenizer; import javax.swing.JOptionPane; public class Discoverer extends Thread implements Runnable { ext.vamsas.IRegistry registry; // the root registry service. 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); } /** * Property change listener firing routine * * @param prop services * @param oldvalue old services hash * @param newvalue new services hash */ public void firePropertyChange(String prop, Object oldvalue, Object newvalue) { changeSupport.firePropertyChange(prop, oldvalue, newvalue); } /** * Initializes the server field with a valid service implementation. * * @return true if service was located. */ private IRegistry locateWebService(java.net.URL WsURL) { IRegistryServiceLocator loc = new IRegistryServiceLocator(); // Default IRegistry server = null; try { server = loc.getRegistryService(WsURL); ( (RegistryServiceSoapBindingStub) server).setTimeout(60000); // One minute timeout } catch (Exception ex) { jalview.bin.Cache.log.error( "Serious! Service location failed\nfor URL :" + WsURL + "\n", ex); return null; } loc.getEngine().setOption("axis", "1"); return server; } static private java.net.URL RootServiceURL = null; static public Vector ServiceURLList = null; static private boolean reallyDiscoverServices = true; public static java.util.Hashtable services = null; // vectors of services stored by abstractServiceType string public static java.util.Vector serviceList = null; // flat list of services static private Vector getDiscoveryURLS() { Vector urls = new Vector(); String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS", "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry"); try{ StringTokenizer st = new StringTokenizer(RootServiceURLs, ","); while (st.hasMoreElements()) { String url = null; try { java.net.URL u = new java.net.URL(url = st.nextToken()); if (!urls.contains(u)) urls.add(u); else jalview.bin.Cache.log.info("Ignoring duplicate url in DISCOVERY_URLS 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 DISCOVERY_URLS 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 DISCOVERY_URLS.",ex);} if (urls.size()>0) return urls; return null; } /** * fetch new services or reset to hardwired defaults depending on preferences. */ static public void doDiscovery() { jalview.bin.Cache.log.debug("(Re)-Initialising the discovery URL list."); try { reallyDiscoverServices = jalview.bin.Cache.getDefault("DISCOVERY_START", false); if (reallyDiscoverServices) { ServiceURLList = getDiscoveryURLS(); } else { jalview.bin.Cache.log.debug("Setting default services"); services = new Hashtable(); // Muscle, Clustal and JPred. ServiceHandle[] defServices = { new ServiceHandle( "MsaWS", "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment " + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.", "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS", "Muscle Multiple Protein Sequence Alignment" ), new ServiceHandle( "MsaWS", "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple" + " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice." + " Nucleic Acids Research, 22 4673-4680", "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS", "ClustalW Multiple Sequence Alignment"), new ServiceHandle( "SecStrPred", "Cuff J. A and Barton G.J (2000) Application of " + "multiple sequence alignment profiles to improve protein secondary structure prediction, " + "Proteins 40:502-511", "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred","JNet Secondary Structure Prediction" )}; services = new Hashtable(); serviceList = new Vector(); buildServiceLists(defServices, serviceList, services); } } catch (Exception e) { System.err.println( "jalview.rootRegistry is not a proper url!\nWas set to " + RootServiceURL + "\n" + e); } } // TODO: JBPNote : make this discover more services based on list of // discovery service urls, break cyclic references to the same url and // duplicate service entries (same endpoint *and* same interface) private ServiceHandle[] getServices(java.net.URL location) { ServiceHandles shs = null; try { jalview.bin.Cache.log.debug("Discovering services using " + location); shs = locateWebService(location).getServices(); } catch (org.apache.axis.AxisFault f) { // JBPNote - should do this a better way! if (f.getFaultReason().indexOf("(407)")>-1) { if (jalview.gui.Desktop.desktop!=null) JOptionPane.showMessageDialog(jalview.gui.Desktop.desktop, "Please set up your proxy settings in the 'Connections' tab of the Preferences window", "Proxy Authorization Failed", JOptionPane.WARNING_MESSAGE); } else { jalview.bin.Cache.log.warn("No Discovery service at " + location); jalview.bin.Cache.log.debug("Axis Fault", f); } } catch (Exception e) { jalview.bin.Cache.log.warn("No Discovery service at " + location); jalview.bin.Cache.log.debug("Discovery Service General Exception", e); } if ( (shs != null) && shs.getServices().length > 0) { return shs.getServices(); } return null; } /** * Adds a list of services to the service catalog and categorised catalog * returns true if ServiceURLList was modified with a new DiscoveryService URL * @param sh ServiceHandle[] * @param cat Vector * @param sscat Hashtable * @return boolean */ static private boolean buildServiceLists(ServiceHandle[] sh, Vector cat, Hashtable sscat) { boolean seenNewDiscovery = false; for (int i = 0, j = sh.length; i < j; i++) { if (!cat.contains(sh[i])) { jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName() + " service called " + sh[i].getName() + " exists at " + sh[i].getEndpointURL() + "\n"); if (!sscat.containsKey(sh[i].getAbstractName())) { sscat.put(sh[i].getAbstractName(), cat = new Vector()); } else { cat = (Vector) sscat.get(sh[i].getAbstractName()); } cat.add(sh[i]); if (sh[i].getAbstractName().equals("Registry")) { for (int s = 0, sUrls = ServiceURLList.size(); s < sUrls; s++) { java.net.URL disc_serv = null; try { disc_serv = new java.net.URL(sh[i].getEndpointURL()); if (!ServiceURLList.contains(disc_serv)) { jalview.bin.Cache.log.debug( "Adding new discovery service at " + disc_serv); ServiceURLList.add(disc_serv); seenNewDiscovery = true; } } catch (Exception e) { jalview.bin.Cache.log.debug( "Ignoring bad discovery service URL " + sh[i].getEndpointURL(), e); } } } } } return seenNewDiscovery; } public void discoverServices() { Hashtable sscat = new Hashtable(); Vector cat = new Vector(); ServiceHandle sh[] = null; int s_url = 0; if (ServiceURLList==null) { jalview.bin.Cache.log.debug("No service endpoints to use for service discovery."); return; } while (s_url < ServiceURLList.size()) { if ( (sh = getServices( (java.net.URL) ServiceURLList.get(s_url))) != null) { buildServiceLists(sh, cat, sscat); } else { jalview.bin.Cache.log.warn( "No services at " +((java.net.URL) ServiceURLList.get(s_url)) +" - check DISCOVERY_URLS property in .jalview_properties"); } s_url++; } // TODO: decide on correct semantics for services list - PropertyChange // provides a way of passing the new object around // so no need to access original discovery thread. // Curent decision is to change properties then notify listeners with old and new values. Hashtable oldServices = services; //Vector oldServicelist = serviceList; services = sscat; serviceList = cat; firePropertyChange("services", oldServices, services); } /** * creates a new thread to call discoverServices() */ public void run() { final Discoverer discoverer = this; Thread discoverThread = new Thread() { public void run() { discoverer.doDiscovery(); discoverer.discoverServices(); } }; discoverThread.start(); } }