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Jws2Discoverer | 63 | 320 | 141 |
1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
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. | |
11 | * | |
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. | |
16 | * | |
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. | |
20 | */ | |
21 | package jalview.ws.jws2; | |
22 | ||
23 | import java.awt.Color; | |
24 | import java.awt.event.ActionEvent; | |
25 | import java.awt.event.ActionListener; | |
26 | import java.beans.PropertyChangeEvent; | |
27 | import java.beans.PropertyChangeListener; | |
28 | import java.beans.PropertyChangeSupport; | |
29 | import java.net.MalformedURLException; | |
30 | import java.net.URL; | |
31 | import java.util.ArrayList; | |
32 | import java.util.Arrays; | |
33 | import java.util.HashMap; | |
34 | import java.util.HashSet; | |
35 | import java.util.Hashtable; | |
36 | import java.util.List; | |
37 | import java.util.Map; | |
38 | import java.util.Set; | |
39 | import java.util.StringTokenizer; | |
40 | import java.util.Vector; | |
41 | ||
42 | import javax.swing.JMenu; | |
43 | import javax.swing.JMenuItem; | |
44 | ||
45 | import compbio.ws.client.Services; | |
46 | import jalview.bin.Cache; | |
47 | import jalview.bin.Console; | |
48 | import jalview.gui.AlignFrame; | |
49 | import jalview.gui.Desktop; | |
50 | import jalview.gui.JvSwingUtils; | |
51 | import jalview.util.MessageManager; | |
52 | import jalview.ws.WSMenuEntryProviderI; | |
53 | import jalview.ws.jws2.jabaws2.Jws2Instance; | |
54 | import jalview.ws.params.ParamDatastoreI; | |
55 | ||
56 | /** | |
57 | * discoverer for jws2 services. Follows the lightweight service discoverer | |
58 | * pattern (archetyped by EnfinEnvision2OneWay) | |
59 | * | |
60 | * @author JimP | |
61 | * | |
62 | */ | |
63 | public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI | |
64 | { | |
65 | public static final String COMPBIO_JABAWS = "http://www.compbio.dundee.ac.uk/jabaws"; | |
66 | ||
67 | /* | |
68 | * the .jalview_properties entry for JWS2 URLS | |
69 | */ | |
70 | private final static String JWS2HOSTURLS = "JWS2HOSTURLS"; | |
71 | ||
72 | /* | |
73 | * Singleton instance | |
74 | */ | |
75 | private static Jws2Discoverer discoverer; | |
76 | ||
77 | /* | |
78 | * Override for testing only | |
79 | */ | |
80 | private static List<String> testUrls = null; | |
81 | ||
82 | // preferred url has precedence over others | |
83 | private String preferredUrl; | |
84 | ||
85 | private PropertyChangeSupport changeSupport = new PropertyChangeSupport( | |
86 | this); | |
87 | ||
88 | private Vector<String> invalidServiceUrls = null; | |
89 | ||
90 | private Vector<String> urlsWithoutServices = null; | |
91 | ||
92 | private Vector<String> validServiceUrls = null; | |
93 | ||
94 | private volatile boolean running = false; | |
95 | ||
96 | private volatile boolean aborted = false; | |
97 | ||
98 | private Thread oldthread = null; | |
99 | ||
100 | /** | |
101 | * holds list of services. | |
102 | */ | |
103 | protected Vector<Jws2Instance> services; | |
104 | ||
105 | /** | |
106 | * Private constructor enforces use of singleton via getDiscoverer() | |
107 | */ | |
108 | 8 | private Jws2Discoverer() |
109 | { | |
110 | } | |
111 | ||
112 | /** | |
113 | * change listeners are notified of "services" property changes | |
114 | * | |
115 | * @param listener | |
116 | * to be added that consumes new services Hashtable object. | |
117 | */ | |
118 | 65 | public void addPropertyChangeListener( |
119 | java.beans.PropertyChangeListener listener) | |
120 | { | |
121 | 65 | changeSupport.addPropertyChangeListener(listener); |
122 | } | |
123 | ||
124 | /** | |
125 | * | |
126 | * | |
127 | * @param listener | |
128 | * to be removed | |
129 | */ | |
130 | 0 | public void removePropertyChangeListener( |
131 | java.beans.PropertyChangeListener listener) | |
132 | { | |
133 | 0 | changeSupport.removePropertyChangeListener(listener); |
134 | } | |
135 | ||
136 | /** | |
137 | * @return the aborted | |
138 | */ | |
139 | 785 | public boolean isAborted() |
140 | { | |
141 | 785 | return aborted; |
142 | } | |
143 | ||
144 | /** | |
145 | * @param aborted | |
146 | * the aborted to set | |
147 | */ | |
148 | 21 | public void setAborted(boolean aborted) |
149 | { | |
150 | 21 | this.aborted = aborted; |
151 | } | |
152 | ||
153 | 65 | @Override |
154 | public void run() | |
155 | { | |
156 | ||
157 | 65 | if (running && oldthread != null && oldthread.isAlive()) |
158 | { | |
159 | 20 | if (!aborted) |
160 | { | |
161 | 0 | return; |
162 | } | |
163 | 41 | while (running) |
164 | { | |
165 | 21 | try |
166 | { | |
167 | 21 | Console.debug( |
168 | "Waiting around for old discovery thread to finish."); | |
169 | // wait around until old discoverer dies | |
170 | 21 | Thread.sleep(100); |
171 | } catch (Exception e) | |
172 | { | |
173 | } | |
174 | } | |
175 | 20 | aborted = false; |
176 | 20 | Console.debug("Old discovery thread has finished."); |
177 | } | |
178 | 65 | running = true; |
179 | ||
180 | // first set up exclusion list if needed | |
181 | 65 | final Set<String> ignoredServices = new HashSet<>(); |
182 | 65 | for (String ignored : Cache |
183 | .getDefault("IGNORED_JABAWS_SERVICETYPES", "").split("\\|")) | |
184 | { | |
185 | 65 | ignoredServices.add(ignored); |
186 | } | |
187 | ||
188 | 65 | changeSupport.firePropertyChange("services", services, |
189 | new Vector<Jws2Instance>()); | |
190 | 65 | oldthread = Thread.currentThread(); |
191 | 65 | try |
192 | { | |
193 | 65 | Class foo = getClass().getClassLoader() |
194 | .loadClass("compbio.ws.client.Jws2Client"); | |
195 | } catch (ClassNotFoundException e) | |
196 | { | |
197 | 0 | jalview.bin.Console.errPrintln( |
198 | "Not enabling JABA Webservices : client jar is not available." | |
199 | + "\nPlease check that your webstart JNLP file is up to date!"); | |
200 | 0 | running = false; |
201 | 0 | return; |
202 | } | |
203 | // reinitialise records of good and bad service URLs | |
204 | 65 | if (services != null) |
205 | { | |
206 | 59 | services.removeAllElements(); |
207 | } | |
208 | 65 | if (urlsWithoutServices != null) |
209 | { | |
210 | 0 | urlsWithoutServices.removeAllElements(); |
211 | } | |
212 | 65 | if (invalidServiceUrls != null) |
213 | { | |
214 | 0 | invalidServiceUrls.removeAllElements(); |
215 | } | |
216 | 65 | if (validServiceUrls != null) |
217 | { | |
218 | 59 | validServiceUrls.removeAllElements(); |
219 | } | |
220 | 65 | ArrayList<String> svctypes = new ArrayList<>(); |
221 | ||
222 | 65 | List<JabaWsServerQuery> qrys = new ArrayList<>(); |
223 | 65 | for (final String jwsserver : getServiceUrls()) |
224 | { | |
225 | 65 | JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsserver); |
226 | 65 | if (svctypes.size() == 0) |
227 | { | |
228 | // TODO: remove this ugly hack to get Canonical JABA service ordering | |
229 | // for all possible services | |
230 | 65 | for (Services sv : squery.JABAWS2SERVERS) |
231 | { | |
232 | 715 | if (!ignoredServices.contains(sv.toString())) |
233 | { | |
234 | 715 | svctypes.add(sv.toString()); |
235 | } | |
236 | } | |
237 | ||
238 | } | |
239 | 65 | qrys.add(squery); |
240 | 65 | new Thread(squery).start(); |
241 | } | |
242 | 65 | boolean finished = true; |
243 | 65 | do |
244 | { | |
245 | 300 | finished = true; |
246 | 300 | try |
247 | { | |
248 | 300 | Thread.sleep(100); |
249 | } catch (Exception e) | |
250 | { | |
251 | } | |
252 | 300 | for (JabaWsServerQuery squery : qrys) |
253 | { | |
254 | 300 | if (squery.isRunning()) |
255 | { | |
256 | 289 | finished = false; |
257 | } | |
258 | } | |
259 | 300 | if (aborted) |
260 | { | |
261 | 56 | Console.debug( |
262 | "Aborting " + qrys.size() + " JABAWS discovery threads."); | |
263 | 56 | for (JabaWsServerQuery squery : qrys) |
264 | { | |
265 | 56 | squery.setQuit(true); |
266 | } | |
267 | } | |
268 | 300 | } while (!aborted && !finished); |
269 | 65 | if (!aborted) |
270 | { | |
271 | // resort services according to order found in jabaws service list | |
272 | // also ensure services for each host are ordered in same way. | |
273 | ||
274 | 9 | if (services != null && services.size() > 0) |
275 | { | |
276 | 9 | Jws2Instance[] svcs = new Jws2Instance[services.size()]; |
277 | 9 | int[] spos = new int[services.size()]; |
278 | 9 | int ipos = 0; |
279 | 9 | List<String> svcUrls = getServiceUrls(); |
280 | 9 | for (Jws2Instance svc : services) |
281 | { | |
282 | 126 | svcs[ipos] = svc; |
283 | 126 | spos[ipos++] = 1000 * svcUrls.indexOf(svc.getHost()) + 1 |
284 | + svctypes.indexOf(svc.serviceType); | |
285 | } | |
286 | 9 | jalview.util.QuickSort.sort(spos, svcs); |
287 | 9 | services = new Vector<>(); |
288 | 9 | for (Jws2Instance svc : svcs) |
289 | { | |
290 | 126 | if (!ignoredServices.contains(svc.serviceType)) |
291 | { | |
292 | 126 | services.add(svc); |
293 | } | |
294 | } | |
295 | } | |
296 | } | |
297 | 65 | oldthread = null; |
298 | 65 | running = false; |
299 | 65 | changeSupport.firePropertyChange("services", new Vector<Jws2Instance>(), |
300 | services); | |
301 | } | |
302 | ||
303 | /** | |
304 | * record this service endpoint so we can use it | |
305 | * | |
306 | * @param jwsservers | |
307 | * @param srv | |
308 | * @param service2 | |
309 | */ | |
310 | 380 | synchronized void addService(String jwsservers, Jws2Instance service) |
311 | { | |
312 | 380 | if (services == null) |
313 | { | |
314 | 6 | services = new Vector<>(); |
315 | } | |
316 | 380 | jalview.bin.Console.info( |
317 | "Discovered service: " + jwsservers + " " + service.toString()); | |
318 | // Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(), | |
319 | // service2); | |
320 | ||
321 | 380 | services.add(service); |
322 | // retrieve the presets and parameter set and cache now | |
323 | 380 | ParamDatastoreI pds = service.getParamStore(); |
324 | 380 | if (pds != null) |
325 | { | |
326 | 380 | pds.getPresets(); |
327 | } | |
328 | 380 | service.hasParameters(); |
329 | 380 | if (validServiceUrls == null) |
330 | { | |
331 | 6 | validServiceUrls = new Vector<>(); |
332 | } | |
333 | 380 | validServiceUrls.add(jwsservers); |
334 | } | |
335 | ||
336 | /** | |
337 | * attach all available web services to the appropriate submenu in the given | |
338 | * JMenu | |
339 | */ | |
340 | 1723 | @Override |
341 | public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame) | |
342 | { | |
343 | // dynamically regenerate service list. | |
344 | 1723 | populateWSMenuEntry(wsmenu, alignFrame, null); |
345 | } | |
346 | ||
347 | 4653 | private boolean isRecalculable(String action) |
348 | { | |
349 | 4653 | return (action != null && action.equalsIgnoreCase("conservation")); |
350 | } | |
351 | ||
352 | 1723 | private void populateWSMenuEntry(JMenu jws2al, |
353 | final AlignFrame alignFrame, String typeFilter) | |
354 | { | |
355 | 1723 | if (running || services == null || services.size() == 0) |
356 | { | |
357 | 0 | return; |
358 | } | |
359 | ||
360 | /** | |
361 | * eventually, JWS2 services will appear under the same align/etc submenus. | |
362 | * for moment we keep them separate. | |
363 | */ | |
364 | 1723 | JMenu atpoint; |
365 | 1723 | List<Jws2Instance> enumerableServices = new ArrayList<>(); |
366 | // jws2al.removeAll(); | |
367 | 1723 | Map<String, Jws2Instance> preferredHosts = new HashMap<>(); |
368 | 1723 | Map<String, List<Jws2Instance>> alternates = new HashMap<>(); |
369 | 1723 | for (Jws2Instance service : services.toArray(new Jws2Instance[0])) |
370 | { | |
371 | 4653 | if (!isRecalculable(service.action)) |
372 | { | |
373 | // add 'one shot' services to be displayed using the classic menu | |
374 | // structure | |
375 | 4610 | enumerableServices.add(service); |
376 | } | |
377 | else | |
378 | { | |
379 | 43 | if (!preferredHosts.containsKey(service.serviceType)) |
380 | { | |
381 | 43 | Jws2Instance preferredInstance = getPreferredServiceFor( |
382 | alignFrame, service.serviceType); | |
383 | 43 | if (preferredInstance != null) |
384 | { | |
385 | 43 | preferredHosts.put(service.serviceType, preferredInstance); |
386 | } | |
387 | else | |
388 | { | |
389 | 0 | preferredHosts.put(service.serviceType, service); |
390 | } | |
391 | } | |
392 | 43 | List<Jws2Instance> ph = alternates.get(service.serviceType); |
393 | 43 | if (preferredHosts.get(service.serviceType) != service) |
394 | { | |
395 | 0 | if (ph == null) |
396 | { | |
397 | 0 | ph = new ArrayList<>(); |
398 | } | |
399 | 0 | ph.add(service); |
400 | 0 | alternates.put(service.serviceType, ph); |
401 | } | |
402 | } | |
403 | ||
404 | } | |
405 | ||
406 | // create GUI element for classic services | |
407 | 1723 | addEnumeratedServices(jws2al, alignFrame, enumerableServices); |
408 | // and the instantaneous services | |
409 | 1721 | for (final Jws2Instance service : preferredHosts.values()) |
410 | { | |
411 | 41 | atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action); |
412 | 41 | JMenuItem hitm; |
413 | 41 | if (atpoint.getItemCount() > 1) |
414 | { | |
415 | // previous service of this type already present | |
416 | 0 | atpoint.addSeparator(); |
417 | } | |
418 | 41 | atpoint.add(hitm = new JMenuItem(service.getHost())); |
419 | 41 | hitm.setForeground(Color.blue); |
420 | 41 | hitm.addActionListener(new ActionListener() |
421 | { | |
422 | ||
423 | 0 | @Override |
424 | public void actionPerformed(ActionEvent e) | |
425 | { | |
426 | 0 | Desktop.showUrl(service.getHost()); |
427 | } | |
428 | }); | |
429 | 41 | hitm.setToolTipText(JvSwingUtils.wrapTooltip(false, |
430 | MessageManager.getString("label.open_jabaws_web_page"))); | |
431 | ||
432 | 41 | service.attachWSMenuEntry(atpoint, alignFrame); |
433 | 37 | if (alternates.containsKey(service.serviceType)) |
434 | { | |
435 | 0 | atpoint.add(hitm = new JMenu( |
436 | MessageManager.getString("label.switch_server"))); | |
437 | 0 | hitm.setToolTipText(JvSwingUtils.wrapTooltip(false, |
438 | MessageManager.getString("label.choose_jabaws_server"))); | |
439 | 0 | for (final Jws2Instance sv : alternates.get(service.serviceType)) |
440 | { | |
441 | 0 | JMenuItem itm; |
442 | 0 | hitm.add(itm = new JMenuItem(sv.getHost())); |
443 | 0 | itm.setForeground(Color.blue); |
444 | 0 | itm.addActionListener(new ActionListener() |
445 | { | |
446 | ||
447 | 0 | @Override |
448 | public void actionPerformed(ActionEvent arg0) | |
449 | { | |
450 | 0 | new Thread(new Runnable() |
451 | { | |
452 | 0 | @Override |
453 | public void run() | |
454 | { | |
455 | 0 | setPreferredServiceFor(alignFrame, sv.serviceType, |
456 | sv.action, sv); | |
457 | 0 | changeSupport.firePropertyChange("services", |
458 | new Vector<Jws2Instance>(), services); | |
459 | } | |
460 | }).start(); | |
461 | ||
462 | } | |
463 | }); | |
464 | } | |
465 | } | |
466 | } | |
467 | } | |
468 | ||
469 | /** | |
470 | * add services using the Java 2.5/2.6/2.7 system which optionally creates | |
471 | * submenus to index by host and service program type | |
472 | */ | |
473 | 1723 | private void addEnumeratedServices(final JMenu jws2al, |
474 | final AlignFrame alignFrame, | |
475 | List<Jws2Instance> enumerableServices) | |
476 | { | |
477 | 1723 | boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), |
478 | bytype = Cache.getDefault("WSMENU_BYTYPE", false); | |
479 | /** | |
480 | * eventually, JWS2 services will appear under the same align/etc submenus. | |
481 | * for moment we keep them separate. | |
482 | */ | |
483 | 1723 | JMenu atpoint; |
484 | ||
485 | 1723 | List<String> hostLabels = new ArrayList<>(); |
486 | 1723 | Hashtable<String, String> lasthostFor = new Hashtable<>(); |
487 | 1723 | Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<>(); |
488 | 1723 | ArrayList<String> hostlist = new ArrayList<>(); |
489 | 1723 | for (Jws2Instance service : enumerableServices) |
490 | { | |
491 | 4610 | ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost()); |
492 | 4610 | if (hostservices == null) |
493 | { | |
494 | 1723 | hosts.put(service.getHost(), hostservices = new ArrayList<>()); |
495 | 1723 | hostlist.add(service.getHost()); |
496 | } | |
497 | 4610 | hostservices.add(service); |
498 | } | |
499 | // now add hosts in order of the given array | |
500 | 1723 | for (String host : hostlist) |
501 | { | |
502 | 1723 | Jws2Instance orderedsvcs[] = hosts.get(host) |
503 | .toArray(new Jws2Instance[1]); | |
504 | 1723 | String sortbytype[] = new String[orderedsvcs.length]; |
505 | 6333 | for (int i = 0; i < sortbytype.length; i++) |
506 | { | |
507 | 4610 | sortbytype[i] = orderedsvcs[i].serviceType; |
508 | } | |
509 | 1723 | jalview.util.QuickSort.sort(sortbytype, orderedsvcs); |
510 | 1723 | for (final Jws2Instance service : orderedsvcs) |
511 | { | |
512 | 4588 | atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action); |
513 | 4588 | String type = service.serviceType; |
514 | 4588 | if (byhost) |
515 | { | |
516 | 0 | atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host); |
517 | 0 | if (atpoint.getToolTipText() == null) |
518 | { | |
519 | 0 | atpoint.setToolTipText(MessageManager |
520 | .formatMessage("label.services_at", new String[] | |
521 | { host })); | |
522 | } | |
523 | } | |
524 | 4588 | if (bytype) |
525 | { | |
526 | 0 | atpoint = JvSwingUtils.findOrCreateMenu(atpoint, type); |
527 | 0 | if (atpoint.getToolTipText() == null) |
528 | { | |
529 | 0 | atpoint.setToolTipText(service.getActionText()); |
530 | } | |
531 | } | |
532 | 4588 | if (!byhost && !hostLabels.contains( |
533 | host + service.serviceType + service.getActionText())) | |
534 | // !hostLabels.contains(host + (bytype ? | |
535 | // service.serviceType+service.getActionText() : ""))) | |
536 | { | |
537 | // add a marker indicating where this service is hosted | |
538 | // relies on services from the same host being listed in a | |
539 | // contiguous | |
540 | // group | |
541 | 4588 | JMenuItem hitm; |
542 | 4588 | if (hostLabels.contains(host)) |
543 | { | |
544 | 2865 | atpoint.addSeparator(); |
545 | } | |
546 | else | |
547 | { | |
548 | 1723 | hostLabels.add(host); |
549 | } | |
550 | 4588 | if (lasthostFor.get(service.action) == null |
551 | || !lasthostFor.get(service.action).equals(host)) | |
552 | { | |
553 | 1808 | atpoint.add(hitm = new JMenuItem(host)); |
554 | 1808 | hitm.setForeground(Color.blue); |
555 | 1808 | hitm.addActionListener(new ActionListener() |
556 | { | |
557 | ||
558 | 0 | @Override |
559 | public void actionPerformed(ActionEvent e) | |
560 | { | |
561 | 0 | Desktop.showUrl(service.getHost()); |
562 | } | |
563 | }); | |
564 | 1808 | hitm.setToolTipText( |
565 | JvSwingUtils.wrapTooltip(true, MessageManager | |
566 | .getString("label.open_jabaws_web_page"))); | |
567 | 1808 | lasthostFor.put(service.action, host); |
568 | } | |
569 | 4588 | hostLabels.add( |
570 | host + service.serviceType + service.getActionText()); | |
571 | } | |
572 | ||
573 | 4588 | service.attachWSMenuEntry(atpoint, alignFrame); |
574 | } | |
575 | } | |
576 | } | |
577 | ||
578 | /** | |
579 | * | |
580 | * @param args | |
581 | * @j2sIgnore | |
582 | */ | |
583 | 0 | public static void main(String[] args) |
584 | { | |
585 | 0 | if (args.length > 0) |
586 | { | |
587 | 0 | testUrls = new ArrayList<>(); |
588 | 0 | for (String url : args) |
589 | { | |
590 | 0 | testUrls.add(url); |
591 | } | |
592 | } | |
593 | 0 | Thread runner = getDiscoverer() |
594 | .startDiscoverer(new PropertyChangeListener() | |
595 | { | |
596 | ||
597 | 0 | @Override |
598 | public void propertyChange(PropertyChangeEvent evt) | |
599 | { | |
600 | 0 | if (getDiscoverer().services != null) |
601 | { | |
602 | 0 | jalview.bin.Console |
603 | .outPrintln("Changesupport: There are now " | |
604 | + getDiscoverer().services.size() | |
605 | + " services"); | |
606 | 0 | int i = 1; |
607 | 0 | for (Jws2Instance instance : getDiscoverer().services) |
608 | { | |
609 | 0 | jalview.bin.Console.outPrintln("Service " + i++ + " " |
610 | + instance.getClass() + "@" + instance.getHost() | |
611 | + ": " + instance.getActionText()); | |
612 | } | |
613 | ||
614 | } | |
615 | } | |
616 | }); | |
617 | 0 | while (runner.isAlive()) |
618 | { | |
619 | 0 | try |
620 | { | |
621 | 0 | Thread.sleep(50); |
622 | } catch (InterruptedException e) | |
623 | { | |
624 | } | |
625 | } | |
626 | 0 | try |
627 | { | |
628 | 0 | Thread.sleep(50); |
629 | } catch (InterruptedException x) | |
630 | { | |
631 | } | |
632 | } | |
633 | ||
634 | /** | |
635 | * Returns the singleton instance of this class. | |
636 | * | |
637 | * @return | |
638 | */ | |
639 | 4422 | public static Jws2Discoverer getDiscoverer() |
640 | { | |
641 | 4422 | if (discoverer == null) |
642 | { | |
643 | 8 | discoverer = new Jws2Discoverer(); |
644 | } | |
645 | 4422 | return discoverer; |
646 | } | |
647 | ||
648 | 2700 | public boolean hasServices() |
649 | { | |
650 | 2700 | return !running && services != null && services.size() > 0; |
651 | } | |
652 | ||
653 | 4414 | public boolean isRunning() |
654 | { | |
655 | 4414 | return running; |
656 | } | |
657 | ||
658 | 0 | public void setServiceUrls(List<String> wsUrls) |
659 | { | |
660 | 0 | if (wsUrls != null && !wsUrls.isEmpty()) |
661 | { | |
662 | 0 | StringBuilder urls = new StringBuilder(128); |
663 | 0 | String sep = ""; |
664 | 0 | for (String url : wsUrls) |
665 | { | |
666 | 0 | urls.append(sep); |
667 | 0 | urls.append(url); |
668 | 0 | sep = ","; |
669 | } | |
670 | 0 | Cache.setProperty(JWS2HOSTURLS, urls.toString()); |
671 | } | |
672 | else | |
673 | { | |
674 | 0 | Cache.removeProperty(JWS2HOSTURLS); |
675 | } | |
676 | } | |
677 | ||
678 | /** | |
679 | * Returns web service URLs, in the order in which they should be tried (or an | |
680 | * empty list). | |
681 | * | |
682 | * @return | |
683 | */ | |
684 | 74 | public List<String> getServiceUrls() |
685 | { | |
686 | 74 | if (testUrls != null) |
687 | { | |
688 | // return test urls, if there are any, instead of touching cache | |
689 | 0 | return testUrls; |
690 | } | |
691 | 74 | List<String> urls = new ArrayList<>(); |
692 | ||
693 | 74 | if (this.preferredUrl != null) |
694 | { | |
695 | 0 | urls.add(preferredUrl); |
696 | } | |
697 | ||
698 | 74 | String surls = Cache.getDefault(JWS2HOSTURLS, COMPBIO_JABAWS); |
699 | 74 | try |
700 | { | |
701 | 74 | StringTokenizer st = new StringTokenizer(surls, ","); |
702 | 148 | while (st.hasMoreElements()) |
703 | { | |
704 | 74 | String url = null; |
705 | 74 | try |
706 | { | |
707 | 74 | url = st.nextToken(); |
708 | 74 | new URL(url); |
709 | 74 | if (!urls.contains(url)) |
710 | { | |
711 | 74 | urls.add(url); |
712 | } | |
713 | else | |
714 | { | |
715 | 0 | Console.warn("Ignoring duplicate url " + url + " in " |
716 | + JWS2HOSTURLS + " list"); | |
717 | } | |
718 | } catch (MalformedURLException ex) | |
719 | { | |
720 | 0 | Console.warn("Problem whilst trying to make a URL from '" |
721 | 0 | + ((url != null) ? url : "<null>") + "'"); |
722 | 0 | Console.warn( |
723 | "This was probably due to a malformed comma separated list" | |
724 | + " in the " + JWS2HOSTURLS | |
725 | + " entry of $(HOME)/.jalview_properties)"); | |
726 | 0 | Console.debug("Exception was ", ex); |
727 | } | |
728 | } | |
729 | } catch (Exception ex) | |
730 | { | |
731 | 0 | Console.warn("Error parsing comma separated list of urls in " |
732 | + JWS2HOSTURLS + " preference.", ex); | |
733 | } | |
734 | 74 | return urls; |
735 | } | |
736 | ||
737 | 1717 | public Vector<Jws2Instance> getServices() |
738 | { | |
739 | 1717 | return (services == null) ? new Vector<>() : new Vector<>(services); |
740 | } | |
741 | ||
742 | /** | |
743 | * test the given URL with the JabaWS test code | |
744 | * | |
745 | * @param foo | |
746 | * @return | |
747 | */ | |
748 | 0 | public static boolean testServiceUrl(URL foo) |
749 | { | |
750 | 0 | try |
751 | { | |
752 | 0 | compbio.ws.client.WSTester |
753 | .main(new String[] | |
754 | { "-h=" + foo.toString() }); | |
755 | } catch (Exception e) | |
756 | { | |
757 | 0 | e.printStackTrace(); |
758 | 0 | return false; |
759 | } catch (OutOfMemoryError e) | |
760 | { | |
761 | 0 | e.printStackTrace(); |
762 | 0 | return false; |
763 | } catch (Error e) | |
764 | { | |
765 | 0 | e.printStackTrace(); |
766 | 0 | return false; |
767 | } | |
768 | ||
769 | 0 | return true; |
770 | } | |
771 | ||
772 | 0 | public boolean restart() |
773 | { | |
774 | 0 | synchronized (this) |
775 | { | |
776 | 0 | if (running) |
777 | { | |
778 | 0 | aborted = true; |
779 | } | |
780 | else | |
781 | { | |
782 | 0 | running = true; |
783 | } | |
784 | 0 | return aborted; |
785 | } | |
786 | } | |
787 | ||
788 | /** | |
789 | * Start a fresh discovery thread and notify the given object when we're | |
790 | * finished. Any known existing threads will be killed before this one is | |
791 | * started. | |
792 | * | |
793 | * @param changeSupport2 | |
794 | * @return new thread | |
795 | */ | |
796 | 65 | public Thread startDiscoverer(PropertyChangeListener changeSupport2) |
797 | { | |
798 | /* if (restart()) | |
799 | { | |
800 | return; | |
801 | } | |
802 | else | |
803 | { | |
804 | Thread thr = new Thread(this); | |
805 | thr.start(); | |
806 | } | |
807 | */ | |
808 | 65 | if (isRunning()) |
809 | { | |
810 | 21 | setAborted(true); |
811 | } | |
812 | 65 | addPropertyChangeListener(changeSupport2); |
813 | 65 | Thread thr = new Thread(this); |
814 | 65 | thr.start(); |
815 | 65 | return thr; |
816 | } | |
817 | ||
818 | /** | |
819 | * @return the invalidServiceUrls | |
820 | */ | |
821 | 34 | public Vector<String> getInvalidServiceUrls() |
822 | { | |
823 | 34 | return invalidServiceUrls; |
824 | } | |
825 | ||
826 | /** | |
827 | * @return the urlsWithoutServices | |
828 | */ | |
829 | 34 | public Vector<String> getUrlsWithoutServices() |
830 | { | |
831 | 34 | return urlsWithoutServices; |
832 | } | |
833 | ||
834 | /** | |
835 | * add an 'empty' JABA server to the list. Only servers not already in the | |
836 | * 'bad URL' list will be added to this list. | |
837 | * | |
838 | * @param jwsservers | |
839 | */ | |
840 | 0 | public synchronized void addUrlwithnoservices(String jwsservers) |
841 | { | |
842 | 0 | if (urlsWithoutServices == null) |
843 | { | |
844 | 0 | urlsWithoutServices = new Vector<>(); |
845 | } | |
846 | ||
847 | 0 | if ((invalidServiceUrls == null |
848 | || !invalidServiceUrls.contains(jwsservers)) | |
849 | && !urlsWithoutServices.contains(jwsservers)) | |
850 | { | |
851 | 0 | urlsWithoutServices.add(jwsservers); |
852 | } | |
853 | } | |
854 | ||
855 | /** | |
856 | * add a bad URL to the list | |
857 | * | |
858 | * @param jwsservers | |
859 | */ | |
860 | 0 | public synchronized void addInvalidServiceUrl(String jwsservers) |
861 | { | |
862 | 0 | if (invalidServiceUrls == null) |
863 | { | |
864 | 0 | invalidServiceUrls = new Vector<>(); |
865 | } | |
866 | 0 | if (!invalidServiceUrls.contains(jwsservers)) |
867 | { | |
868 | 0 | invalidServiceUrls.add(jwsservers); |
869 | } | |
870 | } | |
871 | ||
872 | /** | |
873 | * | |
874 | * @return a human readable report of any problems with the service URLs used | |
875 | * for discovery | |
876 | */ | |
877 | 1655 | public String getErrorMessages() |
878 | { | |
879 | 1655 | if (!isRunning() && !isAborted()) |
880 | { | |
881 | 34 | StringBuffer ermsg = new StringBuffer(); |
882 | 34 | boolean list = false; |
883 | 34 | if (getInvalidServiceUrls() != null |
884 | && getInvalidServiceUrls().size() > 0) | |
885 | { | |
886 | 0 | ermsg.append(MessageManager.getString("warn.urls_not_contacted") |
887 | + ": \n"); | |
888 | 0 | for (String svcurl : getInvalidServiceUrls()) |
889 | { | |
890 | 0 | if (list) |
891 | { | |
892 | 0 | ermsg.append(", "); |
893 | } | |
894 | 0 | list = true; |
895 | 0 | ermsg.append(svcurl); |
896 | } | |
897 | 0 | ermsg.append("\n\n"); |
898 | } | |
899 | 34 | list = false; |
900 | 34 | if (getUrlsWithoutServices() != null |
901 | && getUrlsWithoutServices().size() > 0) | |
902 | { | |
903 | 0 | ermsg.append( |
904 | MessageManager.getString("warn.urls_no_jaba") + ": \n"); | |
905 | 0 | for (String svcurl : getUrlsWithoutServices()) |
906 | { | |
907 | 0 | if (list) |
908 | { | |
909 | 0 | ermsg.append(", "); |
910 | } | |
911 | 0 | list = true; |
912 | 0 | ermsg.append(svcurl); |
913 | } | |
914 | 0 | ermsg.append("\n"); |
915 | } | |
916 | 34 | if (ermsg.length() > 1) |
917 | { | |
918 | 0 | return ermsg.toString(); |
919 | } | |
920 | ||
921 | } | |
922 | 1655 | return null; |
923 | } | |
924 | ||
925 | 0 | public int getServerStatusFor(String url) |
926 | { | |
927 | 0 | if (validServiceUrls != null && validServiceUrls.contains(url)) |
928 | { | |
929 | 0 | return 1; |
930 | } | |
931 | 0 | if (urlsWithoutServices != null && urlsWithoutServices.contains(url)) |
932 | { | |
933 | 0 | return 0; |
934 | } | |
935 | 0 | if (invalidServiceUrls != null && invalidServiceUrls.contains(url)) |
936 | { | |
937 | 0 | return -1; |
938 | } | |
939 | 0 | return -2; |
940 | } | |
941 | ||
942 | /** | |
943 | * pick the user's preferred service based on a set of URLs (jaba server | |
944 | * locations) and service URIs (specifying version and service interface | |
945 | * class) | |
946 | * | |
947 | * @param serviceURL | |
948 | * @return null or best match for given uri/ls. | |
949 | */ | |
950 | 0 | public Jws2Instance getPreferredServiceFor(String[] serviceURLs) |
951 | { | |
952 | 0 | HashSet<String> urls = new HashSet<>(); |
953 | 0 | urls.addAll(Arrays.asList(serviceURLs)); |
954 | 0 | Jws2Instance match = null; |
955 | 0 | if (services != null) |
956 | { | |
957 | 0 | for (Jws2Instance svc : services) |
958 | { | |
959 | 0 | if (urls.contains(svc.getServiceTypeURI())) |
960 | { | |
961 | 0 | if (match == null) |
962 | { | |
963 | // for moment we always pick service from server ordered first in | |
964 | // user's preferences | |
965 | 0 | match = svc; |
966 | } | |
967 | 0 | if (urls.contains(svc.getUri())) |
968 | { | |
969 | // stop and return - we've matched type URI and URI for service | |
970 | // endpoint | |
971 | 0 | return svc; |
972 | } | |
973 | } | |
974 | } | |
975 | } | |
976 | 0 | return match; |
977 | } | |
978 | ||
979 | Map<String, Map<String, String>> preferredServiceMap = new HashMap<>(); | |
980 | ||
981 | /** | |
982 | * get current preferred service of the given type, or global default | |
983 | * | |
984 | * @param af | |
985 | * null or a specific alignFrame | |
986 | * @param serviceType | |
987 | * Jws2Instance.serviceType for service | |
988 | * @return null if no service of this type is available, the preferred service | |
989 | * for the serviceType and af if specified and if defined. | |
990 | */ | |
991 | 43 | public Jws2Instance getPreferredServiceFor(AlignFrame af, |
992 | String serviceType) | |
993 | { | |
994 | 43 | String serviceurl = null; |
995 | 43 | synchronized (preferredServiceMap) |
996 | { | |
997 | 43 | String afid = (af == null) ? "" : af.getViewport().getSequenceSetId(); |
998 | 43 | Map<String, String> prefmap = preferredServiceMap.get(afid); |
999 | 43 | if (afid.length() > 0 && prefmap == null) |
1000 | { | |
1001 | // recover global setting, if any | |
1002 | 43 | prefmap = preferredServiceMap.get(""); |
1003 | } | |
1004 | 43 | if (prefmap != null) |
1005 | { | |
1006 | 0 | serviceurl = prefmap.get(serviceType); |
1007 | } | |
1008 | ||
1009 | } | |
1010 | 43 | Jws2Instance response = null; |
1011 | 43 | for (Jws2Instance svc : services) |
1012 | { | |
1013 | 379 | if (svc.serviceType.equals(serviceType)) |
1014 | { | |
1015 | 43 | if (serviceurl == null || serviceurl.equals(svc.getHost())) |
1016 | { | |
1017 | 43 | response = svc; |
1018 | 43 | break; |
1019 | } | |
1020 | } | |
1021 | } | |
1022 | 43 | return response; |
1023 | } | |
1024 | ||
1025 | 0 | public void setPreferredServiceFor(AlignFrame af, String serviceType, |
1026 | String serviceAction, Jws2Instance selectedServer) | |
1027 | { | |
1028 | 0 | String afid = (af == null) ? "" : af.getViewport().getSequenceSetId(); |
1029 | 0 | if (preferredServiceMap == null) |
1030 | { | |
1031 | 0 | preferredServiceMap = new HashMap<>(); |
1032 | } | |
1033 | 0 | Map<String, String> prefmap = preferredServiceMap.get(afid); |
1034 | 0 | if (prefmap == null) |
1035 | { | |
1036 | 0 | prefmap = new HashMap<>(); |
1037 | 0 | preferredServiceMap.put(afid, prefmap); |
1038 | } | |
1039 | 0 | prefmap.put(serviceType, selectedServer.getHost()); |
1040 | 0 | prefmap.put(serviceAction, selectedServer.getHost()); |
1041 | } | |
1042 | ||
1043 | 0 | public void setPreferredServiceFor(String serviceType, |
1044 | String serviceAction, Jws2Instance selectedServer) | |
1045 | { | |
1046 | 0 | setPreferredServiceFor(null, serviceType, serviceAction, |
1047 | selectedServer); | |
1048 | } | |
1049 | ||
1050 | /** | |
1051 | * Set a URL to try before any others. For use with command-line parameter to | |
1052 | * configure a local Jabaws installation without the need to add to property | |
1053 | * files. | |
1054 | * | |
1055 | * @param value | |
1056 | * @throws MalformedURLException | |
1057 | */ | |
1058 | 2 | public void setPreferredUrl(String value) throws MalformedURLException |
1059 | { | |
1060 | 2 | if (value != null && value.trim().length() > 0) |
1061 | { | |
1062 | 2 | new URL(value); |
1063 | 2 | preferredUrl = value; |
1064 | } | |
1065 | } | |
1066 | } |