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  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.ws.jws2

File Jws2Discoverer.java

 

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148
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1
1,064
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141
0.44
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Classes

Class Line # Actions
Jws2Discoverer 63 323 141 231
0.5452755754.5%
 

Contributing tests

This file is covered by 131 tests. .

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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 jalview.bin.Cache;
24    import jalview.gui.AlignFrame;
25    import jalview.gui.Desktop;
26    import jalview.gui.JvSwingUtils;
27    import jalview.util.MessageManager;
28    import jalview.ws.WSMenuEntryProviderI;
29    import jalview.ws.jws2.jabaws2.Jws2Instance;
30    import jalview.ws.params.ParamDatastoreI;
31   
32    import java.awt.Color;
33    import java.awt.event.ActionEvent;
34    import java.awt.event.ActionListener;
35    import java.beans.PropertyChangeEvent;
36    import java.beans.PropertyChangeListener;
37    import java.beans.PropertyChangeSupport;
38    import java.net.MalformedURLException;
39    import java.net.URL;
40    import java.util.ArrayList;
41    import java.util.Arrays;
42    import java.util.HashMap;
43    import java.util.HashSet;
44    import java.util.Hashtable;
45    import java.util.List;
46    import java.util.Map;
47    import java.util.Set;
48    import java.util.StringTokenizer;
49    import java.util.Vector;
50   
51    import javax.swing.JMenu;
52    import javax.swing.JMenuItem;
53   
54    import compbio.ws.client.Services;
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  1 toggle 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  11 toggle public void addPropertyChangeListener(
119    java.beans.PropertyChangeListener listener)
120    {
121  11 changeSupport.addPropertyChangeListener(listener);
122    }
123   
124    /**
125    *
126    *
127    * @param listener
128    * to be removed
129    */
 
130  0 toggle public void removePropertyChangeListener(
131    java.beans.PropertyChangeListener listener)
132    {
133  0 changeSupport.removePropertyChangeListener(listener);
134    }
135   
136    /**
137    * @return the aborted
138    */
 
139  64 toggle public boolean isAborted()
140    {
141  64 return aborted;
142    }
143   
144    /**
145    * @param aborted
146    * the aborted to set
147    */
 
148  2 toggle public void setAborted(boolean aborted)
149    {
150  2 this.aborted = aborted;
151    }
152   
 
153  11 toggle @Override
154    public void run()
155    {
156   
157  11 if (running && oldthread != null && oldthread.isAlive())
158    {
159  2 if (!aborted)
160    {
161  0 return;
162    }
163  6 while (running)
164    {
165  4 try
166    {
167  4 Cache.log.debug(
168    "Waiting around for old discovery thread to finish.");
169    // wait around until old discoverer dies
170  4 Thread.sleep(100);
171    } catch (Exception e)
172    {
173    }
174    }
175  2 aborted = false;
176  2 Cache.log.debug("Old discovery thread has finished.");
177    }
178  11 running = true;
179   
180    // first set up exclusion list if needed
181  11 final Set<String> ignoredServices = new HashSet<String>();
182  11 for (String ignored : Cache
183    .getDefault("IGNORED_JABAWS_SERVICETYPES", "").split("\\|"))
184    {
185  11 ignoredServices.add(ignored);
186    }
187   
188  11 changeSupport.firePropertyChange("services", services,
189    new Vector<Jws2Instance>());
190  11 oldthread = Thread.currentThread();
191  11 try
192    {
193  11 Class foo = getClass().getClassLoader()
194    .loadClass("compbio.ws.client.Jws2Client");
195    } catch (ClassNotFoundException e)
196    {
197  0 System.err.println(
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  11 if (services != null)
205    {
206  10 services.removeAllElements();
207    }
208  11 if (urlsWithoutServices != null)
209    {
210  0 urlsWithoutServices.removeAllElements();
211    }
212  11 if (invalidServiceUrls != null)
213    {
214  0 invalidServiceUrls.removeAllElements();
215    }
216  11 if (validServiceUrls != null)
217    {
218  10 validServiceUrls.removeAllElements();
219    }
220  11 ArrayList<String> svctypes = new ArrayList<String>();
221   
222  11 List<JabaWsServerQuery> qrys = new ArrayList<JabaWsServerQuery>();
223  11 for (final String jwsserver : getServiceUrls())
224    {
225  11 JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsserver);
226  11 if (svctypes.size() == 0)
227    {
228    // TODO: remove this ugly hack to get Canonical JABA service ordering
229    // for all possible services
230  11 for (Services sv : squery.JABAWS2SERVERS)
231    {
232  121 if (!ignoredServices.contains(sv.toString()))
233    {
234  121 svctypes.add(sv.toString());
235    }
236    }
237   
238    }
239  11 qrys.add(squery);
240  11 new Thread(squery).start();
241    }
242  11 boolean finished = true;
243  11 do
244    {
245  119 finished = true;
246  119 try
247    {
248  119 Thread.sleep(100);
249    } catch (Exception e)
250    {
251    }
252  119 ;
253  119 for (JabaWsServerQuery squery : qrys)
254    {
255  119 if (squery.isRunning())
256    {
257  110 finished = false;
258    }
259    }
260  119 if (aborted)
261    {
262  3 Cache.log.debug(
263    "Aborting " + qrys.size() + " JABAWS discovery threads.");
264  3 for (JabaWsServerQuery squery : qrys)
265    {
266  3 squery.setQuit(true);
267    }
268    }
269  119 } while (!aborted && !finished);
270  11 if (!aborted)
271    {
272    // resort services according to order found in jabaws service list
273    // also ensure services for each host are ordered in same way.
274   
275  8 if (services != null && services.size() > 0)
276    {
277  8 Jws2Instance[] svcs = new Jws2Instance[services.size()];
278  8 int[] spos = new int[services.size()];
279  8 int ipos = 0;
280  8 List<String> svcUrls = getServiceUrls();
281  8 for (Jws2Instance svc : services)
282    {
283  112 svcs[ipos] = svc;
284  112 spos[ipos++] = 1000 * svcUrls.indexOf(svc.getHost()) + 1
285    + svctypes.indexOf(svc.serviceType);
286    }
287  8 jalview.util.QuickSort.sort(spos, svcs);
288  8 services = new Vector<Jws2Instance>();
289  8 for (Jws2Instance svc : svcs)
290    {
291  112 if (!ignoredServices.contains(svc.serviceType))
292    {
293  112 services.add(svc);
294    }
295    }
296    }
297    }
298  11 oldthread = null;
299  11 running = false;
300  11 changeSupport.firePropertyChange("services", new Vector<Jws2Instance>(),
301    services);
302    }
303   
304    /**
305    * record this service endpoint so we can use it
306    *
307    * @param jwsservers
308    * @param srv
309    * @param service2
310    */
 
311  132 toggle synchronized void addService(String jwsservers, Jws2Instance service)
312    {
313  132 if (services == null)
314    {
315  1 services = new Vector<Jws2Instance>();
316    }
317  132 System.out.println(
318    "Discovered service: " + jwsservers + " " + service.toString());
319    // Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
320    // service2);
321   
322  132 services.add(service);
323    // retrieve the presets and parameter set and cache now
324  132 ParamDatastoreI pds = service.getParamStore();
325  132 if (pds != null)
326    {
327  132 pds.getPresets();
328    }
329  132 service.hasParameters();
330  132 if (validServiceUrls == null)
331    {
332  1 validServiceUrls = new Vector<String>();
333    }
334  132 validServiceUrls.add(jwsservers);
335    }
336   
337    /**
338    * attach all available web services to the appropriate submenu in the given
339    * JMenu
340    */
 
341  474 toggle @Override
342    public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
343    {
344    // dynamically regenerate service list.
345  474 populateWSMenuEntry(wsmenu, alignFrame, null);
346    }
347   
 
348  6636 toggle private boolean isRecalculable(String action)
349    {
350  6636 return (action != null && action.equalsIgnoreCase("conservation"));
351    }
352   
 
353  474 toggle private void populateWSMenuEntry(JMenu jws2al,
354    final AlignFrame alignFrame, String typeFilter)
355    {
356  474 if (running || services == null || services.size() == 0)
357    {
358  0 return;
359    }
360   
361    /**
362    * eventually, JWS2 services will appear under the same align/etc submenus.
363    * for moment we keep them separate.
364    */
365  474 JMenu atpoint;
366  474 List<Jws2Instance> enumerableServices = new ArrayList<Jws2Instance>();
367    // jws2al.removeAll();
368  474 Map<String, Jws2Instance> preferredHosts = new HashMap<String, Jws2Instance>();
369  474 Map<String, List<Jws2Instance>> alternates = new HashMap<String, List<Jws2Instance>>();
370  474 for (Jws2Instance service : services.toArray(new Jws2Instance[0]))
371    {
372  6636 if (!isRecalculable(service.action))
373    {
374    // add 'one shot' services to be displayed using the classic menu
375    // structure
376  6162 enumerableServices.add(service);
377    }
378    else
379    {
380  474 if (!preferredHosts.containsKey(service.serviceType))
381    {
382  474 Jws2Instance preferredInstance = getPreferredServiceFor(
383    alignFrame, service.serviceType);
384  474 if (preferredInstance != null)
385    {
386  474 preferredHosts.put(service.serviceType, preferredInstance);
387    }
388    else
389    {
390  0 preferredHosts.put(service.serviceType, service);
391    }
392    }
393  474 List<Jws2Instance> ph = alternates.get(service.serviceType);
394  474 if (preferredHosts.get(service.serviceType) != service)
395    {
396  0 if (ph == null)
397    {
398  0 ph = new ArrayList<Jws2Instance>();
399    }
400  0 ph.add(service);
401  0 alternates.put(service.serviceType, ph);
402    }
403    }
404   
405    }
406   
407    // create GUI element for classic services
408  474 addEnumeratedServices(jws2al, alignFrame, enumerableServices);
409    // and the instantaneous services
410  466 for (final Jws2Instance service : preferredHosts.values())
411    {
412  466 atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
413  466 JMenuItem hitm;
414  466 if (atpoint.getItemCount() > 1)
415    {
416    // previous service of this type already present
417  0 atpoint.addSeparator();
418    }
419  466 atpoint.add(hitm = new JMenuItem(service.getHost()));
420  466 hitm.setForeground(Color.blue);
421  466 hitm.addActionListener(new ActionListener()
422    {
423   
 
424  0 toggle @Override
425    public void actionPerformed(ActionEvent e)
426    {
427  0 Desktop.showUrl(service.getHost());
428    }
429    });
430  466 hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
431    MessageManager.getString("label.open_jabaws_web_page")));
432   
433  466 service.attachWSMenuEntry(atpoint, alignFrame);
434  466 if (alternates.containsKey(service.serviceType))
435    {
436  0 atpoint.add(hitm = new JMenu(
437    MessageManager.getString("label.switch_server")));
438  0 hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
439    MessageManager.getString("label.choose_jabaws_server")));
440  0 for (final Jws2Instance sv : alternates.get(service.serviceType))
441    {
442  0 JMenuItem itm;
443  0 hitm.add(itm = new JMenuItem(sv.getHost()));
444  0 itm.setForeground(Color.blue);
445  0 itm.addActionListener(new ActionListener()
446    {
447   
 
448  0 toggle @Override
449    public void actionPerformed(ActionEvent arg0)
450    {
451  0 new Thread(new Runnable()
452    {
 
453  0 toggle @Override
454    public void run()
455    {
456  0 setPreferredServiceFor(alignFrame, sv.serviceType,
457    sv.action, sv);
458  0 changeSupport.firePropertyChange("services",
459    new Vector<Jws2Instance>(), services);
460    };
461    }).start();
462   
463    }
464    });
465    }
466    }
467    }
468    }
469   
470    /**
471    * add services using the Java 2.5/2.6/2.7 system which optionally creates
472    * submenus to index by host and service program type
473    */
 
474  474 toggle private void addEnumeratedServices(final JMenu jws2al,
475    final AlignFrame alignFrame,
476    List<Jws2Instance> enumerableServices)
477    {
478  474 boolean byhost = Cache.getDefault("WSMENU_BYHOST", false),
479    bytype = Cache.getDefault("WSMENU_BYTYPE", false);
480    /**
481    * eventually, JWS2 services will appear under the same align/etc submenus.
482    * for moment we keep them separate.
483    */
484  474 JMenu atpoint;
485   
486  474 List<String> hostLabels = new ArrayList<String>();
487  474 Hashtable<String, String> lasthostFor = new Hashtable<String, String>();
488  474 Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<String, ArrayList<Jws2Instance>>();
489  474 ArrayList<String> hostlist = new ArrayList<String>();
490  474 for (Jws2Instance service : enumerableServices)
491    {
492  6162 ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
493  6162 if (hostservices == null)
494    {
495  474 hosts.put(service.getHost(),
496    hostservices = new ArrayList<Jws2Instance>());
497  474 hostlist.add(service.getHost());
498    }
499  6162 hostservices.add(service);
500    }
501    // now add hosts in order of the given array
502  474 for (String host : hostlist)
503    {
504  474 Jws2Instance orderedsvcs[] = hosts.get(host)
505    .toArray(new Jws2Instance[1]);
506  474 String sortbytype[] = new String[orderedsvcs.length];
507  6636 for (int i = 0; i < sortbytype.length; i++)
508    {
509  6162 sortbytype[i] = orderedsvcs[i].serviceType;
510    }
511  474 jalview.util.QuickSort.sort(sortbytype, orderedsvcs);
512  474 for (final Jws2Instance service : orderedsvcs)
513    {
514  6074 atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
515  6074 String type = service.serviceType;
516  6074 if (byhost)
517    {
518  0 atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host);
519  0 if (atpoint.getToolTipText() == null)
520    {
521  0 atpoint.setToolTipText(MessageManager
522    .formatMessage("label.services_at", new String[]
523    { host }));
524    }
525    }
526  6074 if (bytype)
527    {
528  0 atpoint = JvSwingUtils.findOrCreateMenu(atpoint, type);
529  0 if (atpoint.getToolTipText() == null)
530    {
531  0 atpoint.setToolTipText(service.getActionText());
532    }
533    }
534  6074 if (!byhost && !hostLabels.contains(
535    host + service.serviceType + service.getActionText()))
536    // !hostLabels.contains(host + (bytype ?
537    // service.serviceType+service.getActionText() : "")))
538    {
539    // add a marker indicating where this service is hosted
540    // relies on services from the same host being listed in a
541    // contiguous
542    // group
543  6074 JMenuItem hitm;
544  6074 if (hostLabels.contains(host))
545    {
546  5600 atpoint.addSeparator();
547    }
548    else
549    {
550  474 hostLabels.add(host);
551    }
552  6074 if (lasthostFor.get(service.action) == null
553    || !lasthostFor.get(service.action).equals(host))
554    {
555  1414 atpoint.add(hitm = new JMenuItem(host));
556  1414 hitm.setForeground(Color.blue);
557  1414 hitm.addActionListener(new ActionListener()
558    {
559   
 
560  0 toggle @Override
561    public void actionPerformed(ActionEvent e)
562    {
563  0 Desktop.showUrl(service.getHost());
564    }
565    });
566  1414 hitm.setToolTipText(
567    JvSwingUtils.wrapTooltip(true, MessageManager
568    .getString("label.open_jabaws_web_page")));
569  1414 lasthostFor.put(service.action, host);
570    }
571  6074 hostLabels.add(
572    host + service.serviceType + service.getActionText());
573    }
574   
575  6074 service.attachWSMenuEntry(atpoint, alignFrame);
576    }
577    }
578    }
579   
 
580  0 toggle public static void main(String[] args)
581    {
582  0 if (args.length > 0)
583    {
584  0 testUrls = new ArrayList<String>();
585  0 for (String url : args)
586    {
587  0 testUrls.add(url);
588    }
589  0 ;
590    }
591  0 Thread runner = getDiscoverer()
592    .startDiscoverer(new PropertyChangeListener()
593    {
594   
 
595  0 toggle @Override
596    public void propertyChange(PropertyChangeEvent evt)
597    {
598  0 if (getDiscoverer().services != null)
599    {
600  0 System.out.println("Changesupport: There are now "
601    + getDiscoverer().services.size() + " services");
602  0 int i = 1;
603  0 for (Jws2Instance instance : getDiscoverer().services)
604    {
605  0 System.out.println("Service " + i++ + " "
606    + instance.getClass() + "@" + instance.getHost()
607    + ": " + instance.getActionText());
608    }
609   
610    }
611    }
612    });
613  0 while (runner.isAlive())
614    {
615  0 try
616    {
617  0 Thread.sleep(50);
618    } catch (InterruptedException e)
619    {
620    }
621  0 ;
622    }
623  0 try
624    {
625  0 Thread.sleep(50);
626    } catch (InterruptedException x)
627    {
628    }
629    }
630   
631    /**
632    * Returns the singleton instance of this class.
633    *
634    * @return
635    */
 
636  1252 toggle public static Jws2Discoverer getDiscoverer()
637    {
638  1252 if (discoverer == null)
639    {
640  1 discoverer = new Jws2Discoverer();
641    }
642  1252 return discoverer;
643    }
644   
 
645  1110 toggle public boolean hasServices()
646    {
647  1110 return !running && services != null && services.size() > 0;
648    }
649   
 
650  1244 toggle public boolean isRunning()
651    {
652  1244 return running;
653    }
654   
 
655  0 toggle public void setServiceUrls(List<String> wsUrls)
656    {
657  0 if (wsUrls != null && !wsUrls.isEmpty())
658    {
659  0 StringBuilder urls = new StringBuilder(128);
660  0 String sep = "";
661  0 for (String url : wsUrls)
662    {
663  0 urls.append(sep);
664  0 urls.append(url);
665  0 sep = ",";
666    }
667  0 Cache.setProperty(JWS2HOSTURLS, urls.toString());
668    }
669    else
670    {
671  0 Cache.removeProperty(JWS2HOSTURLS);
672    }
673    }
674   
675    /**
676    * Returns web service URLs, in the order in which they should be tried (or an
677    * empty list).
678    *
679    * @return
680    */
 
681  19 toggle public List<String> getServiceUrls()
682    {
683  19 if (testUrls != null)
684    {
685    // return test urls, if there are any, instead of touching cache
686  0 return testUrls;
687    }
688  19 List<String> urls = new ArrayList<String>();
689   
690  19 if (this.preferredUrl != null)
691    {
692  0 urls.add(preferredUrl);
693    }
694   
695  19 String surls = Cache.getDefault(JWS2HOSTURLS, COMPBIO_JABAWS);
696  19 try
697    {
698  19 StringTokenizer st = new StringTokenizer(surls, ",");
699  38 while (st.hasMoreElements())
700    {
701  19 String url = null;
702  19 try
703    {
704  19 url = st.nextToken();
705  19 new URL(url);
706  19 if (!urls.contains(url))
707    {
708  19 urls.add(url);
709    }
710    else
711    {
712  0 Cache.log.warn("Ignoring duplicate url " + url + " in "
713    + JWS2HOSTURLS + " list");
714    }
715    } catch (MalformedURLException ex)
716    {
717  0 Cache.log.warn("Problem whilst trying to make a URL from '"
718  0 + ((url != null) ? url : "<null>") + "'");
719  0 Cache.log.warn(
720    "This was probably due to a malformed comma separated list"
721    + " in the " + JWS2HOSTURLS
722    + " entry of $(HOME)/.jalview_properties)");
723  0 Cache.log.debug("Exception was ", ex);
724    }
725    }
726    } catch (Exception ex)
727    {
728  0 Cache.log.warn("Error parsing comma separated list of urls in "
729    + JWS2HOSTURLS + " preference.", ex);
730    }
731  19 return urls;
732    }
733   
 
734  466 toggle public Vector<Jws2Instance> getServices()
735    {
736  466 return (services == null) ? new Vector<Jws2Instance>()
737    : new Vector<Jws2Instance>(services);
738    }
739   
740    /**
741    * test the given URL with the JabaWS test code
742    *
743    * @param foo
744    * @return
745    */
 
746  0 toggle public static boolean testServiceUrl(URL foo)
747    {
748  0 try
749    {
750  0 compbio.ws.client.WSTester
751    .main(new String[]
752    { "-h=" + foo.toString() });
753    } catch (Exception e)
754    {
755  0 e.printStackTrace();
756  0 return false;
757    } catch (OutOfMemoryError e)
758    {
759  0 e.printStackTrace();
760  0 return false;
761    } catch (Error e)
762    {
763  0 e.printStackTrace();
764  0 return false;
765    }
766   
767  0 return true;
768    }
769   
 
770  0 toggle public boolean restart()
771    {
772  0 synchronized (this)
773    {
774  0 if (running)
775    {
776  0 aborted = true;
777    }
778    else
779    {
780  0 running = true;
781    }
782  0 return aborted;
783    }
784    }
785   
786    /**
787    * Start a fresh discovery thread and notify the given object when we're
788    * finished. Any known existing threads will be killed before this one is
789    * started.
790    *
791    * @param changeSupport2
792    * @return new thread
793    */
 
794  11 toggle public Thread startDiscoverer(PropertyChangeListener changeSupport2)
795    {
796    /* if (restart())
797    {
798    return;
799    }
800    else
801    {
802    Thread thr = new Thread(this);
803    thr.start();
804    }
805    */
806  11 if (isRunning())
807    {
808  2 setAborted(true);
809    }
810  11 addPropertyChangeListener(changeSupport2);
811  11 Thread thr = new Thread(this);
812  11 thr.start();
813  11 return thr;
814    }
815   
816    /**
817    * @return the invalidServiceUrls
818    */
 
819  53 toggle public Vector<String> getInvalidServiceUrls()
820    {
821  53 return invalidServiceUrls;
822    }
823   
824    /**
825    * @return the urlsWithoutServices
826    */
 
827  53 toggle public Vector<String> getUrlsWithoutServices()
828    {
829  53 return urlsWithoutServices;
830    }
831   
832    /**
833    * add an 'empty' JABA server to the list. Only servers not already in the
834    * 'bad URL' list will be added to this list.
835    *
836    * @param jwsservers
837    */
 
838  0 toggle public synchronized void addUrlwithnoservices(String jwsservers)
839    {
840  0 if (urlsWithoutServices == null)
841    {
842  0 urlsWithoutServices = new Vector<String>();
843    }
844   
845  0 if ((invalidServiceUrls == null
846    || !invalidServiceUrls.contains(jwsservers))
847    && !urlsWithoutServices.contains(jwsservers))
848    {
849  0 urlsWithoutServices.add(jwsservers);
850    }
851    }
852   
853    /**
854    * add a bad URL to the list
855    *
856    * @param jwsservers
857    */
 
858  0 toggle public synchronized void addInvalidServiceUrl(String jwsservers)
859    {
860  0 if (invalidServiceUrls == null)
861    {
862  0 invalidServiceUrls = new Vector<String>();
863    }
864  0 if (!invalidServiceUrls.contains(jwsservers))
865    {
866  0 invalidServiceUrls.add(jwsservers);
867    }
868    }
869   
870    /**
871    *
872    * @return a human readable report of any problems with the service URLs used
873    * for discovery
874    */
 
875  131 toggle public String getErrorMessages()
876    {
877  131 if (!isRunning() && !isAborted())
878    {
879  53 StringBuffer ermsg = new StringBuffer();
880  53 boolean list = false;
881  53 if (getInvalidServiceUrls() != null
882    && getInvalidServiceUrls().size() > 0)
883    {
884  0 ermsg.append(MessageManager.getString("warn.urls_not_contacted")
885    + ": \n");
886  0 for (String svcurl : getInvalidServiceUrls())
887    {
888  0 if (list)
889    {
890  0 ermsg.append(", ");
891    }
892  0 list = true;
893  0 ermsg.append(svcurl);
894    }
895  0 ermsg.append("\n\n");
896    }
897  53 list = false;
898  53 if (getUrlsWithoutServices() != null
899    && getUrlsWithoutServices().size() > 0)
900    {
901  0 ermsg.append(
902    MessageManager.getString("warn.urls_no_jaba") + ": \n");
903  0 for (String svcurl : getUrlsWithoutServices())
904    {
905  0 if (list)
906    {
907  0 ermsg.append(", ");
908    }
909  0 list = true;
910  0 ermsg.append(svcurl);
911    }
912  0 ermsg.append("\n");
913    }
914  53 if (ermsg.length() > 1)
915    {
916  0 return ermsg.toString();
917    }
918   
919    }
920  131 return null;
921    }
922   
 
923  0 toggle public int getServerStatusFor(String url)
924    {
925  0 if (validServiceUrls != null && validServiceUrls.contains(url))
926    {
927  0 return 1;
928    }
929  0 if (urlsWithoutServices != null && urlsWithoutServices.contains(url))
930    {
931  0 return 0;
932    }
933  0 if (invalidServiceUrls != null && invalidServiceUrls.contains(url))
934    {
935  0 return -1;
936    }
937  0 return -2;
938    }
939   
940    /**
941    * pick the user's preferred service based on a set of URLs (jaba server
942    * locations) and service URIs (specifying version and service interface
943    * class)
944    *
945    * @param serviceURL
946    * @return null or best match for given uri/ls.
947    */
 
948  0 toggle public Jws2Instance getPreferredServiceFor(String[] serviceURLs)
949    {
950  0 HashSet<String> urls = new HashSet<String>();
951  0 urls.addAll(Arrays.asList(serviceURLs));
952  0 Jws2Instance match = null;
953  0 if (services != null)
954    {
955  0 for (Jws2Instance svc : services)
956    {
957  0 if (urls.contains(svc.getServiceTypeURI()))
958    {
959  0 if (match == null)
960    {
961    // for moment we always pick service from server ordered first in
962    // user's preferences
963  0 match = svc;
964    }
965  0 if (urls.contains(svc.getUri()))
966    {
967    // stop and return - we've matched type URI and URI for service
968    // endpoint
969  0 return svc;
970    }
971    }
972    }
973    }
974  0 return match;
975    }
976   
977    Map<String, Map<String, String>> preferredServiceMap = new HashMap<String, Map<String, String>>();;
978   
979    /**
980    * get current preferred service of the given type, or global default
981    *
982    * @param af
983    * null or a specific alignFrame
984    * @param serviceType
985    * Jws2Instance.serviceType for service
986    * @return null if no service of this type is available, the preferred service
987    * for the serviceType and af if specified and if defined.
988    */
 
989  474 toggle public Jws2Instance getPreferredServiceFor(AlignFrame af,
990    String serviceType)
991    {
992  474 String serviceurl = null;
993  474 synchronized (preferredServiceMap)
994    {
995  474 String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
996  474 Map<String, String> prefmap = preferredServiceMap.get(afid);
997  474 if (afid.length() > 0 && prefmap == null)
998    {
999    // recover global setting, if any
1000  474 prefmap = preferredServiceMap.get("");
1001    }
1002  474 if (prefmap != null)
1003    {
1004  0 serviceurl = prefmap.get(serviceType);
1005    }
1006   
1007    }
1008  474 Jws2Instance response = null;
1009  474 for (Jws2Instance svc : services)
1010    {
1011  4266 if (svc.serviceType.equals(serviceType))
1012    {
1013  474 if (serviceurl == null || serviceurl.equals(svc.getHost()))
1014    {
1015  474 response = svc;
1016  474 break;
1017    }
1018    }
1019    }
1020  474 return response;
1021    }
1022   
 
1023  0 toggle public void setPreferredServiceFor(AlignFrame af, String serviceType,
1024    String serviceAction, Jws2Instance selectedServer)
1025    {
1026  0 String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
1027  0 if (preferredServiceMap == null)
1028    {
1029  0 preferredServiceMap = new HashMap<String, Map<String, String>>();
1030    }
1031  0 Map<String, String> prefmap = preferredServiceMap.get(afid);
1032  0 if (prefmap == null)
1033    {
1034  0 prefmap = new HashMap<String, String>();
1035  0 preferredServiceMap.put(afid, prefmap);
1036    }
1037  0 prefmap.put(serviceType, selectedServer.getHost());
1038  0 prefmap.put(serviceAction, selectedServer.getHost());
1039    }
1040   
 
1041  0 toggle public void setPreferredServiceFor(String serviceType,
1042    String serviceAction, Jws2Instance selectedServer)
1043    {
1044  0 setPreferredServiceFor(null, serviceType, serviceAction,
1045    selectedServer);
1046    }
1047   
1048    /**
1049    * Set a URL to try before any others. For use with command-line parameter to
1050    * configure a local Jabaws installation without the need to add to property
1051    * files.
1052    *
1053    * @param value
1054    * @throws MalformedURLException
1055    */
 
1056  0 toggle public void setPreferredUrl(String value) throws MalformedURLException
1057    {
1058  0 if (value != null && value.trim().length() > 0)
1059    {
1060  0 new URL(value);
1061  0 preferredUrl = value;
1062    }
1063    }
1064    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.