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
41 public static Discoverer getInstance()
43 Instance j = Instance.getInstance();
44 return (j.discoverer == null ? j.discoverer = new Discoverer()
53 private java.net.URL RootServiceURL = null;
55 private Vector<URL> ServiceURLList = null;
57 private boolean reallyDiscoverServices = true;
59 private Hashtable<String, Vector<ServiceHandle>> services = null;
61 public Hashtable<String, Vector<ServiceHandle>> getServices()
66 private Vector<ServiceHandle> serviceList = null;
68 // private ext.vamsas.IRegistry registry; // the root registry service.
71 private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
75 * change listeners are notified of "services" property changes
78 * to be added that consumes new services Hashtable object.
80 public void addPropertyChangeListener(
81 java.beans.PropertyChangeListener listener)
83 changeSupport.addPropertyChangeListener(listener);
92 public void removePropertyChangeListener(
93 java.beans.PropertyChangeListener listener)
95 changeSupport.removePropertyChangeListener(listener);
99 * Property change listener firing routine
108 public void firePropertyChange(String prop, Object oldvalue,
111 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
115 * Initializes the server field with a valid service implementation.
117 * @return true if service was located.
119 private IRegistry locateWebService(java.net.URL WsURL)
121 IRegistryServiceLocator loc = new IRegistryServiceLocator(); // Default
122 IRegistry server = null;
125 server = loc.getRegistryService(WsURL);
126 ((RegistryServiceSoapBindingStub) server).setTimeout(60000); // One
129 } catch (Exception ex)
131 jalview.bin.Cache.log.error(
132 "Serious! Service location failed\nfor URL :" + WsURL + "\n",
138 loc.getEngine().setOption("axis", "1");
143 static private Vector<URL> getDiscoveryURLS()
145 Vector<URL> urls = new Vector<>();
146 String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS",
147 "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
151 StringTokenizer st = new StringTokenizer(RootServiceURLs, ",");
152 while (st.hasMoreElements())
157 java.net.URL u = new java.net.URL(url = st.nextToken());
158 if (!urls.contains(u))
164 jalview.bin.Cache.log
165 .info("Ignoring duplicate url in DISCOVERY_URLS list");
167 } catch (Exception ex)
169 jalview.bin.Cache.log
170 .warn("Problem whilst trying to make a URL from '"
171 + ((url != null) ? url : "<null>") + "'");
172 jalview.bin.Cache.log.warn(
173 "This was probably due to a malformed comma separated list"
174 + " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
175 jalview.bin.Cache.log.debug("Exception was ", ex);
178 } catch (Exception ex)
180 jalview.bin.Cache.log.warn(
181 "Error parsing comma separated list of urls in DISCOVERY_URLS.",
192 * fetch new services or reset to hardwired defaults depending on preferences.
194 static public void doDiscovery()
196 jalview.bin.Cache.log
197 .debug("(Re)-Initialising the discovery URL list.");
198 Discoverer d = getInstance();
201 d.reallyDiscoverServices = jalview.bin.Cache
202 .getDefault("DISCOVERY_START", false);
203 if (d.reallyDiscoverServices)
205 d.ServiceURLList = getDiscoveryURLS();
209 jalview.bin.Cache.log.debug("Setting default services");
210 d.services = new Hashtable<>();
211 // Muscle, Clustal and JPred.
212 ServiceHandle[] defServices = { new ServiceHandle("MsaWS",
213 "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment "
214 + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
215 "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
216 MessageManager.getString(
217 "label.muscle_multiple_protein_sequence_alignment")),
218 new ServiceHandle("MsaWS",
219 "Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) "
220 + "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\""
221 + " Nucleic Acids Research, 33 511-518",
222 "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS",
223 MessageManager.getString(
224 "label.mafft_multiple_sequence_alignment")),
225 new ServiceHandle("MsaWS",
226 "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"
227 + " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
228 + " Nucleic Acids Research, 22 4673-4680",
229 "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
230 MessageManager.getString(
231 "label.clustalw_multiple_sequence_alignment")),
232 new ServiceHandle("SecStrPred",
233 "Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)\nJPred4: a protein secondary structure prediction server"
234 + "\nNucleic Acids Research, Web Server issue (first published 15th April 2015)"
235 + "\ndoi://10.1093/nar/gkv332",
236 "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred",
237 "JPred Secondary Structure Prediction") };
238 d.services = new Hashtable<>();
239 d.serviceList = new Vector<>();
240 buildServiceLists(defServices, d.serviceList, d.services);
243 } catch (Exception e)
246 "jalview.rootRegistry is not a proper url!\nWas set to "
247 + d.RootServiceURL + "\n" + e);
252 // TODO: JBPNote : make this discover more services based on list of
253 // discovery service urls, break cyclic references to the same url and
254 // duplicate service entries (same endpoint *and* same interface)
255 private ServiceHandle[] getServices(java.net.URL location)
257 ServiceHandles shs = null;
260 jalview.bin.Cache.log.debug("Discovering services using " + location);
261 shs = locateWebService(location).getServices();
262 } catch (org.apache.axis.AxisFault f)
264 // JBPNote - should do this a better way!
265 if (f.getFaultReason().indexOf("(407)") > -1)
267 if (jalview.gui.Desktop.getDesktopPane() != null)
269 JvOptionPane.showMessageDialog(jalview.gui.Desktop.getDesktopPane(),
270 MessageManager.getString("label.set_proxy_settings"),
272 .getString("label.proxy_authorization_failed"),
273 JvOptionPane.WARNING_MESSAGE);
278 jalview.bin.Cache.log.warn("No Discovery service at " + location);
279 jalview.bin.Cache.log.debug("Axis Fault", f);
281 } catch (Exception e)
283 jalview.bin.Cache.log.warn("No Discovery service at " + location);
284 jalview.bin.Cache.log.debug("Discovery Service General Exception", e);
286 if ((shs != null) && shs.getServices().length > 0)
288 return shs.getServices();
294 * Adds a list of services to the service catalog and categorised catalog
295 * returns true if ServiceURLList was modified with a new DiscoveryService URL
305 static private boolean buildServiceLists(ServiceHandle[] sh,
306 Vector<ServiceHandle> cat,
307 Hashtable<String, Vector<ServiceHandle>> sscat)
309 boolean seenNewDiscovery = false;
310 for (int i = 0, j = sh.length; i < j; i++)
312 if (!cat.contains(sh[i]))
314 jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName()
315 + " service called " + sh[i].getName() + " exists at "
316 + sh[i].getEndpointURL() + "\n");
317 if (!sscat.containsKey(sh[i].getAbstractName()))
319 sscat.put(sh[i].getAbstractName(), cat = new Vector<>());
323 cat = sscat.get(sh[i].getAbstractName());
326 if (sh[i].getAbstractName().equals("Registry"))
328 Vector<URL> list = getInstance().ServiceURLList;
329 for (int s = 0, sUrls = list.size(); s < sUrls; s++)
331 java.net.URL disc_serv = null;
334 disc_serv = new java.net.URL(sh[i].getEndpointURL());
335 if (!list.contains(disc_serv))
337 jalview.bin.Cache.log.debug(
338 "Adding new discovery service at " + disc_serv);
340 seenNewDiscovery = true;
342 } catch (Exception e)
344 jalview.bin.Cache.log
345 .debug("Ignoring bad discovery service URL "
346 + sh[i].getEndpointURL(), e);
352 return seenNewDiscovery;
355 public void discoverServices()
357 Hashtable<String, Vector<ServiceHandle>> sscat = new Hashtable<>();
358 Vector<ServiceHandle> cat = new Vector<>();
359 ServiceHandle sh[] = null;
361 if (ServiceURLList == null)
363 jalview.bin.Cache.log
364 .debug("No service endpoints to use for service discovery.");
367 while (s_url < ServiceURLList.size())
369 if ((sh = getServices(
370 ServiceURLList.get(s_url))) != null)
373 buildServiceLists(sh, cat, sscat);
377 jalview.bin.Cache.log.warn("No services at "
378 + (ServiceURLList.get(s_url))
379 + " - check DISCOVERY_URLS property in .jalview_properties");
383 // TODO: decide on correct semantics for services list - PropertyChange
384 // provides a way of passing the new object around
385 // so no need to access original discovery thread.
386 // Curent decision is to change properties then notify listeners with old
388 Hashtable<String, Vector<ServiceHandle>> oldServices = services;
389 // Vector oldServicelist = serviceList;
392 changeSupport.firePropertyChange("services", oldServices, services);
396 * creates a new thread to call discoverServices()
401 final Discoverer discoverer = this;
402 Thread discoverThread = new Thread()
407 Discoverer.doDiscovery();
408 discoverer.discoverServices();
411 discoverThread.start();
415 * binding service abstract name to handler class
417 private static Hashtable<String, WS1Client> serviceClientBindings;
419 public static WS1Client getServiceClient(ServiceHandle sh)
421 if (serviceClientBindings == null)
423 // get a list from Config or create below
424 serviceClientBindings = new Hashtable<>();
425 serviceClientBindings.put("MsaWS", new MsaWSClient());
426 serviceClientBindings.put("SecStrPred", new JPredClient());
427 serviceClientBindings.put("SeqSearch", new SeqSearchWSClient());
429 WS1Client instance = serviceClientBindings
430 .get(sh.getAbstractName());
431 if (instance == null)
434 "WARNING - POSSIBLE IMPLEMENTATION ERROR - cannot find WSClient implementation for "
435 + sh.getAbstractName());
439 instance.serviceHandle = sh;
444 * notes on discovery service 1. need to allow multiple discovery source urls.
445 * 2. user interface to add/control list of urls in preferences notes on
446 * wsclient discovery 1. need a classpath property with list of additional
447 * plugin directories 2. optional config to cite specific bindings between
448 * class name and Abstract service name. 3. precedence for automatic discovery
449 * by using getAbstractName for WSClient - user added plugins override default
450 * plugins ? notes on wsclient gui code for gui attachment now moved to
451 * wsclient implementation. Needs more abstraction but approach seems to work.
452 * is it possible to 'generalise' the data retrieval calls further ? current
453 * methods are very specific (gatherForMSA or gatherForSeqOrMsaSecStrPred),
454 * new methods for conservation (group or alignment), treecalc (aligned
455 * profile), seqannot (sequences selected from dataset, annotation back to