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;
24 import java.util.Hashtable;
25 import java.util.StringTokenizer;
26 import java.util.Vector;
28 import ext.vamsas.IRegistry;
29 import ext.vamsas.IRegistryServiceLocator;
30 import ext.vamsas.RegistryServiceSoapBindingStub;
31 import ext.vamsas.ServiceHandle;
32 import ext.vamsas.ServiceHandles;
33 import jalview.bin.Cache;
34 import jalview.bin.ApplicationSingletonProvider;
35 import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
36 import jalview.gui.JvOptionPane;
37 import jalview.util.MessageManager;
39 public class Discoverer implements Runnable, ApplicationSingletonI
42 public static Discoverer getInstance()
44 return (Discoverer) ApplicationSingletonProvider.getInstance(Discoverer.class);
52 ext.vamsas.IRegistry registry; // the root registry service.
54 private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
58 * change listeners are notified of "services" property changes
61 * to be added that consumes new services Hashtable object.
63 public void addPropertyChangeListener(
64 java.beans.PropertyChangeListener listener)
66 changeSupport.addPropertyChangeListener(listener);
75 public void removePropertyChangeListener(
76 java.beans.PropertyChangeListener listener)
78 changeSupport.removePropertyChangeListener(listener);
82 * Property change listener firing routine
91 public void firePropertyChange(String prop, Object oldvalue,
94 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
98 * Initializes the server field with a valid service implementation.
100 * @return true if service was located.
102 private IRegistry locateWebService(java.net.URL WsURL)
104 IRegistryServiceLocator loc = new IRegistryServiceLocator(); // Default
105 IRegistry server = null;
108 server = loc.getRegistryService(WsURL);
109 ((RegistryServiceSoapBindingStub) server).setTimeout(60000); // One
112 } catch (Exception ex)
114 jalview.bin.Cache.log.error(
115 "Serious! Service location failed\nfor URL :" + WsURL + "\n",
121 loc.getEngine().setOption("axis", "1");
126 private java.net.URL RootServiceURL = null;
128 private Vector<URL> ServiceURLList = null;
130 public Vector<URL> getServiceURLList() {
131 return ServiceURLList;
134 private boolean reallyDiscoverServices = true;
136 private java.util.Hashtable<String, Vector<ServiceHandle>> services = null;
138 // abstractServiceType
141 public java.util.Vector<ServiceHandle> serviceList = null;
143 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 getInstance().discovery();
199 private void discovery()
201 jalview.bin.Cache.log
202 .debug("(Re)-Initialising the discovery URL list.");
205 Discoverer d = getInstance();
206 reallyDiscoverServices = jalview.bin.Cache
207 .getDefault("DISCOVERY_START", false);
208 if (reallyDiscoverServices)
210 ServiceURLList = getDiscoveryURLS();
214 jalview.bin.Cache.log.debug("Setting default services");
215 services = new Hashtable<>();
216 // Muscle, Clustal and JPred.
217 ServiceHandle[] defServices = { new ServiceHandle("MsaWS",
218 "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment "
219 + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
220 "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
221 MessageManager.getString(
222 "label.muscle_multiple_protein_sequence_alignment")),
223 new ServiceHandle("MsaWS",
224 "Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) "
225 + "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\""
226 + " Nucleic Acids Research, 33 511-518",
227 "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS",
228 MessageManager.getString(
229 "label.mafft_multiple_sequence_alignment")),
230 new ServiceHandle("MsaWS",
231 "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"
232 + " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
233 + " Nucleic Acids Research, 22 4673-4680",
234 "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
235 MessageManager.getString(
236 "label.clustalw_multiple_sequence_alignment")),
237 new ServiceHandle("SecStrPred",
238 "Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)\nJPred4: a protein secondary structure prediction server"
239 + "\nNucleic Acids Research, Web Server issue (first published 15th April 2015)"
240 + "\ndoi://10.1093/nar/gkv332",
241 "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred",
242 "JPred Secondary Structure Prediction") };
243 services = new Hashtable<>();
244 serviceList = new Vector<>();
245 buildServiceLists(defServices, serviceList, services);
248 } catch (Exception e)
251 "jalview.rootRegistry is not a proper url!\nWas set to "
252 + RootServiceURL + "\n" + e);
257 // TODO: JBPNote : make this discover more services based on list of
258 // discovery service urls, break cyclic references to the same url and
259 // duplicate service entries (same endpoint *and* same interface)
260 private ServiceHandle[] getServices(java.net.URL location)
262 ServiceHandles shs = null;
265 jalview.bin.Cache.log.debug("Discovering services using " + location);
266 shs = locateWebService(location).getServices();
267 } catch (org.apache.axis.AxisFault f)
269 // JBPNote - should do this a better way!
270 if (f.getFaultReason().indexOf("(407)") > -1)
272 if (jalview.gui.Desktop.getDesktopPane() != null)
274 JvOptionPane.showMessageDialog(jalview.gui.Desktop.getDesktopPane(),
275 MessageManager.getString("label.set_proxy_settings"),
277 .getString("label.proxy_authorization_failed"),
278 JvOptionPane.WARNING_MESSAGE);
283 jalview.bin.Cache.log.warn("No Discovery service at " + location);
284 jalview.bin.Cache.log.debug("Axis Fault", f);
286 } catch (Exception e)
288 jalview.bin.Cache.log.warn("No Discovery service at " + location);
289 jalview.bin.Cache.log.debug("Discovery Service General Exception", e);
291 if ((shs != null) && shs.getServices().length > 0)
293 return shs.getServices();
299 * Adds a list of services to the service catalog and categorised catalog
300 * returns true if ServiceURLList was modified with a new DiscoveryService URL
310 private boolean buildServiceLists(ServiceHandle[] sh,
311 Vector<ServiceHandle> cat,
312 Hashtable<String, Vector<ServiceHandle>> sscat)
314 boolean seenNewDiscovery = false;
315 for (int i = 0, j = sh.length; i < j; i++)
317 if (!cat.contains(sh[i]))
319 jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName()
320 + " service called " + sh[i].getName() + " exists at "
321 + sh[i].getEndpointURL() + "\n");
322 if (!sscat.containsKey(sh[i].getAbstractName()))
324 sscat.put(sh[i].getAbstractName(), cat = new Vector<>());
328 cat = sscat.get(sh[i].getAbstractName());
331 if (sh[i].getAbstractName().equals("Registry"))
333 for (int s = 0, sUrls = ServiceURLList.size(); s < sUrls; s++)
335 java.net.URL disc_serv = null;
338 disc_serv = new java.net.URL(sh[i].getEndpointURL());
339 if (!ServiceURLList.contains(disc_serv))
341 jalview.bin.Cache.log.debug(
342 "Adding new discovery service at " + disc_serv);
343 ServiceURLList.add(disc_serv);
344 seenNewDiscovery = true;
346 } catch (Exception e)
348 jalview.bin.Cache.log
349 .debug("Ignoring bad discovery service URL "
350 + sh[i].getEndpointURL(), e);
356 return seenNewDiscovery;
359 public void discoverServices()
361 Hashtable<String, Vector<ServiceHandle>> sscat = new Hashtable<>();
362 Vector<ServiceHandle> cat = new Vector<>();
363 ServiceHandle sh[] = null;
365 if (ServiceURLList == null)
367 jalview.bin.Cache.log
368 .debug("No service endpoints to use for service discovery.");
371 while (s_url < ServiceURLList.size())
373 if ((sh = getServices(
374 ServiceURLList.get(s_url))) != null)
377 buildServiceLists(sh, cat, sscat);
381 jalview.bin.Cache.log.warn("No services at "
382 + (ServiceURLList.get(s_url))
383 + " - check DISCOVERY_URLS property in .jalview_properties");
387 // TODO: decide on correct semantics for services list - PropertyChange
388 // provides a way of passing the new object around
389 // so no need to access original discovery thread.
390 // Curent decision is to change properties then notify listeners with old
392 Hashtable<String, Vector<ServiceHandle>> oldServices = services;
393 // Vector oldServicelist = serviceList;
396 changeSupport.firePropertyChange("services", oldServices, services);
400 * creates a new thread to call discoverServices()
405 Cache.log.info("Discovering jws1 services");
406 Discoverer.doDiscovery();
411 * binding service abstract name to handler class
413 private Hashtable<String, WS1Client> serviceClientBindings;
415 public static WS1Client getServiceClient(ServiceHandle sh)
417 return getInstance().getClient(sh);
421 * notes on discovery service 1. need to allow multiple discovery source urls.
422 * 2. user interface to add/control list of urls in preferences notes on
423 * wsclient discovery 1. need a classpath property with list of additional
424 * plugin directories 2. optional config to cite specific bindings between
425 * class name and Abstract service name. 3. precedence for automatic discovery
426 * by using getAbstractName for WSClient - user added plugins override default
427 * plugins ? notes on wsclient gui code for gui attachment now moved to
428 * wsclient implementation. Needs more abstraction but approach seems to work.
429 * is it possible to 'generalise' the data retrieval calls further ? current
430 * methods are very specific (gatherForMSA or gatherForSeqOrMsaSecStrPred),
431 * new methods for conservation (group or alignment), treecalc (aligned
432 * profile), seqannot (sequences selected from dataset, annotation back to
437 private WS1Client getClient(ServiceHandle sh)
439 if (serviceClientBindings == null)
441 // get a list from Config or create below
442 serviceClientBindings = new Hashtable<>();
443 serviceClientBindings.put("MsaWS", new MsaWSClient());
444 serviceClientBindings.put("SecStrPred", new JPredClient());
445 serviceClientBindings.put("SeqSearch", new SeqSearchWSClient());
447 WS1Client instance = serviceClientBindings
448 .get(sh.getAbstractName());
449 if (instance == null)
452 "WARNING - POSSIBLE IMPLEMENTATION ERROR - cannot find WSClient implementation for "
453 + sh.getAbstractName());
457 instance.serviceHandle = sh;
462 public static Hashtable<String, Vector<ServiceHandle>> getServices()
464 return getInstance().services;