2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
3 * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 * <p>Description: </p>
26 * <p>Copyright: Copyright (c) 2004</p>
28 * <p>Company: Dundee University</p>
30 * @author not attributable
39 public class Discoverer
40 extends Thread implements Runnable
42 ext.vamsas.IRegistry registry; // the root registry service.
43 private java.beans.PropertyChangeSupport changeSupport = new java.beans.
44 PropertyChangeSupport(this);
47 * change listeners are notified of "services" property changes
49 * @param listener to be added that consumes new services Hashtable object.
51 public void addPropertyChangeListener(
52 java.beans.PropertyChangeListener listener)
54 changeSupport.addPropertyChangeListener(listener);
60 * @param listener to be removed
62 public void removePropertyChangeListener(
63 java.beans.PropertyChangeListener listener)
65 changeSupport.removePropertyChangeListener(listener);
69 * Property change listener firing routine
71 * @param prop services
72 * @param oldvalue old services hash
73 * @param newvalue new services hash
75 public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
77 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
81 * Initializes the server field with a valid service implementation.
83 * @return true if service was located.
85 private IRegistry locateWebService(java.net.URL WsURL)
87 IRegistryServiceLocator loc = new IRegistryServiceLocator(); // Default
88 IRegistry server = null;
91 server = loc.getRegistryService(WsURL);
92 ( (RegistryServiceSoapBindingStub) server).setTimeout(60000); // One minute timeout
96 jalview.bin.Cache.log.error(
97 "Serious! Service location failed\nfor URL :" + WsURL +
103 loc.getEngine().setOption("axis", "1");
108 static private java.net.URL RootServiceURL = null;
109 static public Vector ServiceURLList = null;
110 static private boolean reallyDiscoverServices = true;
112 public static java.util.Hashtable services = null; // vectors of services stored by abstractServiceType string
113 public static java.util.Vector serviceList = null; // flat list of services
114 static private Vector getDiscoveryURLS()
116 Vector urls = new Vector();
117 String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS",
118 "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
122 StringTokenizer st = new StringTokenizer(RootServiceURLs, ",");
123 while (st.hasMoreElements())
128 java.net.URL u = new java.net.URL(url = st.nextToken());
129 if (!urls.contains(u))
135 jalview.bin.Cache.log.info(
136 "Ignoring duplicate url in DISCOVERY_URLS list");
141 jalview.bin.Cache.log.warn(
142 "Problem whilst trying to make a URL from '" +
143 ( (url != null) ? url : "<null>") + "'");
144 jalview.bin.Cache.log.warn(
145 "This was probably due to a malformed comma separated list"
146 + " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
147 jalview.bin.Cache.log.debug("Exception was ", ex);
153 jalview.bin.Cache.log.warn(
154 "Error parsing comma separated list of urls in DISCOVERY_URLS.", ex);
164 * fetch new services or reset to hardwired defaults depending on preferences.
166 static public void doDiscovery()
168 jalview.bin.Cache.log.debug("(Re)-Initialising the discovery URL list.");
171 reallyDiscoverServices = jalview.bin.Cache.getDefault("DISCOVERY_START", false);
172 if (reallyDiscoverServices)
174 ServiceURLList = getDiscoveryURLS();
178 jalview.bin.Cache.log.debug("Setting default services");
179 services = new Hashtable();
180 // Muscle, Clustal and JPred.
181 ServiceHandle[] defServices =
185 "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment " +
186 "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
187 "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
188 "Muscle Multiple Protein Sequence Alignment"
192 "Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) " +
193 "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\"" +
194 " Nucleic Acids Research, 33 511-518",
195 "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS",
196 "MAFFT Multiple Sequence Alignment"),
199 "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple" +
200 " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice." +
201 " Nucleic Acids Research, 22 4673-4680",
202 "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
203 "ClustalW Multiple Sequence Alignment"),
206 "Cole C., Barber J. D., Barton G.J (2008) "
207 +"The Jpred 3 secondary structure prediction server "
208 +"Nucleic Acids Research, 36 W197-W201",
209 "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred",
210 "JNet Secondary Structure Prediction"
212 services = new Hashtable();
213 serviceList = new Vector();
214 buildServiceLists(defServices, serviceList, services);
221 "jalview.rootRegistry is not a proper url!\nWas set to " +
222 RootServiceURL + "\n" + e);
227 // TODO: JBPNote : make this discover more services based on list of
228 // discovery service urls, break cyclic references to the same url and
229 // duplicate service entries (same endpoint *and* same interface)
230 private ServiceHandle[] getServices(java.net.URL location)
232 ServiceHandles shs = null;
235 jalview.bin.Cache.log.debug("Discovering services using " + location);
236 shs = locateWebService(location).getServices();
238 catch (org.apache.axis.AxisFault f)
240 // JBPNote - should do this a better way!
241 if (f.getFaultReason().indexOf("(407)") > -1)
243 if (jalview.gui.Desktop.desktop != null)
245 JOptionPane.showMessageDialog(jalview.gui.Desktop.desktop, "Please set up your proxy settings in the 'Connections' tab of the Preferences window",
246 "Proxy Authorization Failed",
247 JOptionPane.WARNING_MESSAGE);
252 jalview.bin.Cache.log.warn("No Discovery service at " +
254 jalview.bin.Cache.log.debug("Axis Fault", f);
259 jalview.bin.Cache.log.warn("No Discovery service at " +
261 jalview.bin.Cache.log.debug("Discovery Service General Exception", e);
263 if ( (shs != null) && shs.getServices().length > 0)
265 return shs.getServices();
271 * Adds a list of services to the service catalog and categorised catalog
272 * returns true if ServiceURLList was modified with a new DiscoveryService URL
273 * @param sh ServiceHandle[]
275 * @param sscat Hashtable
278 static private boolean buildServiceLists(ServiceHandle[] sh, Vector cat,
281 boolean seenNewDiscovery = false;
282 for (int i = 0, j = sh.length; i < j; i++)
284 if (!cat.contains(sh[i]))
286 jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName() +
288 sh[i].getName() + " exists at " +
289 sh[i].getEndpointURL() + "\n");
290 if (!sscat.containsKey(sh[i].getAbstractName()))
292 sscat.put(sh[i].getAbstractName(), cat = new Vector());
296 cat = (Vector) sscat.get(sh[i].getAbstractName());
299 if (sh[i].getAbstractName().equals("Registry"))
301 for (int s = 0, sUrls = ServiceURLList.size(); s < sUrls; s++)
303 java.net.URL disc_serv = null;
306 disc_serv = new java.net.URL(sh[i].getEndpointURL());
307 if (!ServiceURLList.contains(disc_serv))
309 jalview.bin.Cache.log.debug(
310 "Adding new discovery service at " + disc_serv);
311 ServiceURLList.add(disc_serv);
312 seenNewDiscovery = true;
317 jalview.bin.Cache.log.debug(
318 "Ignoring bad discovery service URL " + sh[i].getEndpointURL(),
325 return seenNewDiscovery;
328 public void discoverServices()
330 Hashtable sscat = new Hashtable();
331 Vector cat = new Vector();
332 ServiceHandle sh[] = null;
334 if (ServiceURLList == null)
336 jalview.bin.Cache.log.debug(
337 "No service endpoints to use for service discovery.");
340 while (s_url < ServiceURLList.size())
342 if ( (sh = getServices( (java.net.URL) ServiceURLList.get(s_url))) != null)
345 buildServiceLists(sh, cat, sscat);
349 jalview.bin.Cache.log.warn(
351 + ( (java.net.URL) ServiceURLList.get(s_url))
352 + " - check DISCOVERY_URLS property in .jalview_properties");
356 // TODO: decide on correct semantics for services list - PropertyChange
357 // provides a way of passing the new object around
358 // so no need to access original discovery thread.
359 // Curent decision is to change properties then notify listeners with old and new values.
360 Hashtable oldServices = services;
361 //Vector oldServicelist = serviceList;
364 firePropertyChange("services", oldServices, services);
368 * creates a new thread to call discoverServices()
372 final Discoverer discoverer = this;
373 Thread discoverThread = new Thread()
377 discoverer.doDiscovery();
378 discoverer.discoverServices();
381 discoverThread.start();
384 * binding service abstract name to handler class
386 private static Hashtable serviceClientBindings;
387 public static WSClient getServiceClient(ServiceHandle sh)
389 if (serviceClientBindings==null)
391 // get a list from Config or create below
392 serviceClientBindings = new Hashtable();
393 serviceClientBindings.put("MsaWS",new MsaWSClient());
394 serviceClientBindings.put("SecStrPred",new JPredClient());
395 serviceClientBindings.put("SeqSearch",new SeqSearchWSClient());
397 WSClient instance = (WSClient) serviceClientBindings.get(sh.getAbstractName());
400 System.err.println("WARNING - POSSIBLE IMPLEMENTATION ERROR - cannot find WSClient implementation for "+sh.getAbstractName());
403 instance.serviceHandle = sh;
408 * notes on discovery service
409 * 1. need to allow multiple discovery source urls.
410 * 2. user interface to add/control list of urls in preferences
411 * notes on wsclient discovery
412 * 1. need a classpath property with list of additional plugin directories
413 * 2. optional config to cite specific bindings between class name and Abstract service name.
414 * 3. precedence for automatic discovery by using getAbstractName for WSClient - user added plugins override default plugins ?
415 * notes on wsclient gui
416 * code for gui attachment now moved to wsclient implementation. Needs more abstraction but approach seems to work.
417 * is it possible to 'generalise' the data retrieval calls further ? current methods are very specific (gatherForMSA or gatherForSeqOrMsaSecStrPred), new methods for conservation (group or alignment), treecalc (aligned profile), seqannot (sequences selected from dataset, annotation back to dataset).