2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ws.jws1;
23 import jalview.bin.Instance;
24 import jalview.gui.JvOptionPane;
25 import jalview.util.MessageManager;
28 import java.util.Hashtable;
29 import java.util.StringTokenizer;
30 import java.util.Vector;
32 import ext.vamsas.IRegistry;
33 import ext.vamsas.IRegistryServiceLocator;
34 import ext.vamsas.RegistryServiceSoapBindingStub;
35 import ext.vamsas.ServiceHandle;
36 import ext.vamsas.ServiceHandles;
38 public class Discoverer implements Runnable
45 public static Discoverer getInstance()
47 Instance j = Instance.getInstance();
48 return (j.discoverer == null ? j.discoverer = new Discoverer()
52 private java.net.URL RootServiceURL = null;
54 private Vector<URL> ServiceURLList = null;
56 private boolean reallyDiscoverServices = true;
58 private Hashtable<String, Vector<ServiceHandle>> services = null;
60 public Hashtable<String, Vector<ServiceHandle>> getServices()
65 private Vector<ServiceHandle> serviceList = null;
67 // private ext.vamsas.IRegistry registry; // the root registry service.
70 private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
74 * change listeners are notified of "services" property changes
77 * to be added that consumes new services Hashtable object.
79 public void addPropertyChangeListener(
80 java.beans.PropertyChangeListener listener)
82 changeSupport.addPropertyChangeListener(listener);
91 public void removePropertyChangeListener(
92 java.beans.PropertyChangeListener listener)
94 changeSupport.removePropertyChangeListener(listener);
98 * Property change listener firing routine
107 public void firePropertyChange(String prop, Object oldvalue,
110 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
114 * Initializes the server field with a valid service implementation.
116 * @return true if service was located.
118 private IRegistry locateWebService(java.net.URL WsURL)
120 IRegistryServiceLocator loc = new IRegistryServiceLocator(); // Default
121 IRegistry server = null;
124 server = loc.getRegistryService(WsURL);
125 ((RegistryServiceSoapBindingStub) server).setTimeout(60000); // One
128 } catch (Exception ex)
130 jalview.bin.Cache.log.error(
131 "Serious! Service location failed\nfor URL :" + WsURL + "\n",
137 loc.getEngine().setOption("axis", "1");
142 static private Vector<URL> getDiscoveryURLS()
144 Vector<URL> urls = new Vector<>();
145 String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS",
146 "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
150 StringTokenizer st = new StringTokenizer(RootServiceURLs, ",");
151 while (st.hasMoreElements())
156 java.net.URL u = new java.net.URL(url = st.nextToken());
157 if (!urls.contains(u))
163 jalview.bin.Cache.log
164 .info("Ignoring duplicate url in DISCOVERY_URLS list");
166 } catch (Exception ex)
168 jalview.bin.Cache.log
169 .warn("Problem whilst trying to make a URL from '"
170 + ((url != null) ? url : "<null>") + "'");
171 jalview.bin.Cache.log.warn(
172 "This was probably due to a malformed comma separated list"
173 + " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
174 jalview.bin.Cache.log.debug("Exception was ", ex);
177 } catch (Exception ex)
179 jalview.bin.Cache.log.warn(
180 "Error parsing comma separated list of urls in DISCOVERY_URLS.",
191 * fetch new services or reset to hardwired defaults depending on preferences.
193 static public void doDiscovery()
195 jalview.bin.Cache.log
196 .debug("(Re)-Initialising the discovery URL list.");
197 Discoverer d = getInstance();
200 d.reallyDiscoverServices = jalview.bin.Cache
201 .getDefault("DISCOVERY_START", false);
202 if (d.reallyDiscoverServices)
204 d.ServiceURLList = getDiscoveryURLS();
208 jalview.bin.Cache.log.debug("Setting default services");
209 d.services = new Hashtable<>();
210 // Muscle, Clustal and JPred.
211 ServiceHandle[] defServices = { new ServiceHandle("MsaWS",
212 "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment "
213 + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
214 "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
215 MessageManager.getString(
216 "label.muscle_multiple_protein_sequence_alignment")),
217 new ServiceHandle("MsaWS",
218 "Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) "
219 + "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\""
220 + " Nucleic Acids Research, 33 511-518",
221 "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS",
222 MessageManager.getString(
223 "label.mafft_multiple_sequence_alignment")),
224 new ServiceHandle("MsaWS",
225 "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"
226 + " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
227 + " Nucleic Acids Research, 22 4673-4680",
228 "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
229 MessageManager.getString(
230 "label.clustalw_multiple_sequence_alignment")),
231 new ServiceHandle("SecStrPred",
232 "Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)\nJPred4: a protein secondary structure prediction server"
233 + "\nNucleic Acids Research, Web Server issue (first published 15th April 2015)"
234 + "\ndoi://10.1093/nar/gkv332",
235 "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred",
236 "JPred Secondary Structure Prediction") };
237 d.services = new Hashtable<>();
238 d.serviceList = new Vector<>();
239 buildServiceLists(defServices, d.serviceList, d.services);
242 } catch (Exception e)
245 "jalview.rootRegistry is not a proper url!\nWas set to "
246 + d.RootServiceURL + "\n" + e);
251 // TODO: JBPNote : make this discover more services based on list of
252 // discovery service urls, break cyclic references to the same url and
253 // duplicate service entries (same endpoint *and* same interface)
254 private ServiceHandle[] getServices(java.net.URL location)
256 ServiceHandles shs = null;
259 jalview.bin.Cache.log.debug("Discovering services using " + location);
260 shs = locateWebService(location).getServices();
261 } catch (org.apache.axis.AxisFault f)
263 // JBPNote - should do this a better way!
264 if (f.getFaultReason().indexOf("(407)") > -1)
266 if (jalview.gui.Desktop.getDesktopPane() != null)
268 JvOptionPane.showMessageDialog(jalview.gui.Desktop.getDesktopPane(),
269 MessageManager.getString("label.set_proxy_settings"),
271 .getString("label.proxy_authorization_failed"),
272 JvOptionPane.WARNING_MESSAGE);
277 jalview.bin.Cache.log.warn("No Discovery service at " + location);
278 jalview.bin.Cache.log.debug("Axis Fault", f);
280 } catch (Exception e)
282 jalview.bin.Cache.log.warn("No Discovery service at " + location);
283 jalview.bin.Cache.log.debug("Discovery Service General Exception", e);
285 if ((shs != null) && shs.getServices().length > 0)
287 return shs.getServices();
293 * Adds a list of services to the service catalog and categorised catalog
294 * returns true if ServiceURLList was modified with a new DiscoveryService URL
304 static private boolean buildServiceLists(ServiceHandle[] sh,
305 Vector<ServiceHandle> cat,
306 Hashtable<String, Vector<ServiceHandle>> sscat)
308 boolean seenNewDiscovery = false;
309 for (int i = 0, j = sh.length; i < j; i++)
311 if (!cat.contains(sh[i]))
313 jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName()
314 + " service called " + sh[i].getName() + " exists at "
315 + sh[i].getEndpointURL() + "\n");
316 if (!sscat.containsKey(sh[i].getAbstractName()))
318 sscat.put(sh[i].getAbstractName(), cat = new Vector<>());
322 cat = sscat.get(sh[i].getAbstractName());
325 if (sh[i].getAbstractName().equals("Registry"))
327 Vector<URL> list = getInstance().ServiceURLList;
328 for (int s = 0, sUrls = list.size(); s < sUrls; s++)
330 java.net.URL disc_serv = null;
333 disc_serv = new java.net.URL(sh[i].getEndpointURL());
334 if (!list.contains(disc_serv))
336 jalview.bin.Cache.log.debug(
337 "Adding new discovery service at " + disc_serv);
339 seenNewDiscovery = true;
341 } catch (Exception e)
343 jalview.bin.Cache.log
344 .debug("Ignoring bad discovery service URL "
345 + sh[i].getEndpointURL(), e);
351 return seenNewDiscovery;
354 public void discoverServices()
356 Hashtable<String, Vector<ServiceHandle>> sscat = new Hashtable<>();
357 Vector<ServiceHandle> cat = new Vector<>();
358 ServiceHandle sh[] = null;
360 if (ServiceURLList == null)
362 jalview.bin.Cache.log
363 .debug("No service endpoints to use for service discovery.");
366 while (s_url < ServiceURLList.size())
368 if ((sh = getServices(
369 ServiceURLList.get(s_url))) != null)
372 buildServiceLists(sh, cat, sscat);
376 jalview.bin.Cache.log.warn("No services at "
377 + (ServiceURLList.get(s_url))
378 + " - check DISCOVERY_URLS property in .jalview_properties");
382 // TODO: decide on correct semantics for services list - PropertyChange
383 // provides a way of passing the new object around
384 // so no need to access original discovery thread.
385 // Curent decision is to change properties then notify listeners with old
387 Hashtable<String, Vector<ServiceHandle>> oldServices = services;
388 // Vector oldServicelist = serviceList;
391 changeSupport.firePropertyChange("services", oldServices, services);
395 * creates a new thread to call discoverServices()
400 final Discoverer discoverer = this;
401 Thread discoverThread = new Thread()
406 Discoverer.doDiscovery();
407 discoverer.discoverServices();
410 discoverThread.start();
414 * binding service abstract name to handler class
416 private static Hashtable<String, WS1Client> serviceClientBindings;
418 public static WS1Client getServiceClient(ServiceHandle sh)
420 if (serviceClientBindings == null)
422 // get a list from Config or create below
423 serviceClientBindings = new Hashtable<>();
424 serviceClientBindings.put("MsaWS", new MsaWSClient());
425 serviceClientBindings.put("SecStrPred", new JPredClient());
426 serviceClientBindings.put("SeqSearch", new SeqSearchWSClient());
428 WS1Client instance = serviceClientBindings
429 .get(sh.getAbstractName());
430 if (instance == null)
433 "WARNING - POSSIBLE IMPLEMENTATION ERROR - cannot find WSClient implementation for "
434 + sh.getAbstractName());
438 instance.serviceHandle = sh;
443 * notes on discovery service 1. need to allow multiple discovery source urls.
444 * 2. user interface to add/control list of urls in preferences notes on
445 * wsclient discovery 1. need a classpath property with list of additional
446 * plugin directories 2. optional config to cite specific bindings between
447 * class name and Abstract service name. 3. precedence for automatic discovery
448 * by using getAbstractName for WSClient - user added plugins override default
449 * plugins ? notes on wsclient gui code for gui attachment now moved to
450 * wsclient implementation. Needs more abstraction but approach seems to work.
451 * is it possible to 'generalise' the data retrieval calls further ? current
452 * methods are very specific (gatherForMSA or gatherForSeqOrMsaSecStrPred),
453 * new methods for conservation (group or alignment), treecalc (aligned
454 * profile), seqannot (sequences selected from dataset, annotation back to