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.jws2;
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;
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;
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;
48 import java.util.StringTokenizer;
49 import java.util.Vector;
51 import javax.swing.JMenu;
52 import javax.swing.JMenuItem;
54 import compbio.ws.client.Services;
57 * discoverer for jws2 services. Follows the lightweight service discoverer
58 * pattern (archetyped by EnfinEnvision2OneWay)
63 public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
65 public static final String COMPBIO_JABAWS = "http://www.compbio.dundee.ac.uk/jabaws";
68 * the .jalview_properties entry for JWS2 URLS
70 private final static String JWS2HOSTURLS = "JWS2HOSTURLS";
75 private static Jws2Discoverer discoverer;
78 * Override for testing only
80 private static List<String> testUrls = null;
82 // preferred url has precedence over others
83 private String preferredUrl;
85 private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
88 private Vector<String> invalidServiceUrls = null;
90 private Vector<String> urlsWithoutServices = null;
92 private Vector<String> validServiceUrls = null;
94 private volatile boolean running = false;
96 private volatile boolean aborted = false;
98 private Thread oldthread = null;
101 * holds list of services.
103 protected Vector<Jws2Instance> services;
106 * Private constructor enforces use of singleton via getDiscoverer()
108 private Jws2Discoverer()
113 * change listeners are notified of "services" property changes
116 * to be added that consumes new services Hashtable object.
118 public void addPropertyChangeListener(
119 java.beans.PropertyChangeListener listener)
121 changeSupport.addPropertyChangeListener(listener);
130 public void removePropertyChangeListener(
131 java.beans.PropertyChangeListener listener)
133 changeSupport.removePropertyChangeListener(listener);
137 * @return the aborted
139 public boolean isAborted()
148 public void setAborted(boolean aborted)
150 this.aborted = aborted;
157 if (running && oldthread != null && oldthread.isAlive())
168 "Waiting around for old discovery thread to finish.");
169 // wait around until old discoverer dies
171 } catch (Exception e)
176 Cache.log.debug("Old discovery thread has finished.");
180 // first set up exclusion list if needed
181 final Set<String> ignoredServices = new HashSet<>();
182 for (String ignored : Cache
183 .getDefault("IGNORED_JABAWS_SERVICETYPES", "").split("\\|"))
185 ignoredServices.add(ignored);
188 changeSupport.firePropertyChange("services", services,
189 new Vector<Jws2Instance>());
190 oldthread = Thread.currentThread();
193 Class foo = getClass().getClassLoader()
194 .loadClass("compbio.ws.client.Jws2Client");
195 } catch (ClassNotFoundException e)
198 "Not enabling JABA Webservices : client jar is not available."
199 + "\nPlease check that your webstart JNLP file is up to date!");
203 // reinitialise records of good and bad service URLs
204 if (services != null)
206 services.removeAllElements();
208 if (urlsWithoutServices != null)
210 urlsWithoutServices.removeAllElements();
212 if (invalidServiceUrls != null)
214 invalidServiceUrls.removeAllElements();
216 if (validServiceUrls != null)
218 validServiceUrls.removeAllElements();
220 ArrayList<String> svctypes = new ArrayList<>();
222 List<JabaWsServerQuery> qrys = new ArrayList<>();
223 for (final String jwsserver : getServiceUrls())
225 JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsserver);
226 if (svctypes.size() == 0)
228 // TODO: remove this ugly hack to get Canonical JABA service ordering
229 // for all possible services
230 for (Services sv : squery.JABAWS2SERVERS)
232 if (!ignoredServices.contains(sv.toString()))
234 svctypes.add(sv.toString());
240 new Thread(squery).start();
242 boolean finished = true;
249 } catch (Exception e)
253 for (JabaWsServerQuery squery : qrys)
255 if (squery.isRunning())
263 "Aborting " + qrys.size() + " JABAWS discovery threads.");
264 for (JabaWsServerQuery squery : qrys)
266 squery.setQuit(true);
269 } while (!aborted && !finished);
272 // resort services according to order found in jabaws service list
273 // also ensure services for each host are ordered in same way.
275 if (services != null && services.size() > 0)
277 Jws2Instance[] svcs = new Jws2Instance[services.size()];
278 int[] spos = new int[services.size()];
280 List<String> svcUrls = getServiceUrls();
281 for (Jws2Instance svc : services)
284 spos[ipos++] = 1000 * svcUrls.indexOf(svc.getHostURL()) + 1
285 + svctypes.indexOf(svc.getName());
287 jalview.util.QuickSort.sort(spos, svcs);
288 services = new Vector<>();
289 for (Jws2Instance svc : svcs)
291 if (!ignoredServices.contains(svc.getName()))
300 changeSupport.firePropertyChange("services", new Vector<Jws2Instance>(),
305 * record this service endpoint so we can use it
311 synchronized void addService(String jwsservers, Jws2Instance service)
313 if (services == null)
315 services = new Vector<>();
318 "Discovered service: " + jwsservers + " " + service.toString());
319 // Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
322 services.add(service);
323 // retrieve the presets and parameter set and cache now
324 ParamDatastoreI pds = service.getParamStore();
329 service.hasParameters();
330 if (validServiceUrls == null)
332 validServiceUrls = new Vector<>();
334 validServiceUrls.add(jwsservers);
338 * attach all available web services to the appropriate submenu in the given
342 public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
344 // dynamically regenerate service list.
345 populateWSMenuEntry(wsmenu, alignFrame, null);
348 private boolean isRecalculable(String action)
350 return (action != null && action.equalsIgnoreCase("conservation"));
353 private void populateWSMenuEntry(JMenu jws2al,
354 final AlignFrame alignFrame, String typeFilter)
356 if (running || services == null || services.size() == 0)
362 * eventually, JWS2 services will appear under the same align/etc submenus.
363 * for moment we keep them separate.
366 List<Jws2Instance> enumerableServices = new ArrayList<>();
367 // jws2al.removeAll();
368 Map<String, Jws2Instance> preferredHosts = new HashMap<>();
369 Map<String, List<Jws2Instance>> alternates = new HashMap<>();
370 for (Jws2Instance service : services.toArray(new Jws2Instance[0]))
372 // TODO: check this behaves with refactored serviceType to getName
373 if (!isRecalculable(service.getName()))
375 // add 'one shot' services to be displayed using the classic menu
377 enumerableServices.add(service);
381 if (!preferredHosts.containsKey(service.getName()))
383 Jws2Instance preferredInstance = getPreferredServiceFor(
384 alignFrame, service.getName());
385 if (preferredInstance != null)
387 preferredHosts.put(service.getName(), preferredInstance);
391 preferredHosts.put(service.getName(), service);
394 List<Jws2Instance> ph = alternates.get(service.getName());
395 if (preferredHosts.get(service.getName()) != service)
399 ph = new ArrayList<>();
402 alternates.put(service.getName(), ph);
408 // create GUI element for classic services
409 addEnumeratedServices(jws2al, alignFrame, enumerableServices);
410 // and the instantaneous services
411 for (final Jws2Instance service : preferredHosts.values())
413 atpoint = JvSwingUtils.findOrCreateMenu(jws2al,
414 service.getServiceType());
416 if (atpoint.getItemCount() > 1)
418 // previous service of this type already present
419 atpoint.addSeparator();
421 atpoint.add(hitm = new JMenuItem(service.getHostURL()));
422 hitm.setForeground(Color.blue);
423 hitm.addActionListener(new ActionListener()
427 public void actionPerformed(ActionEvent e)
429 Desktop.showUrl(service.getHostURL());
432 hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
433 MessageManager.getString("label.open_jabaws_web_page")));
435 service.attachWSMenuEntry(atpoint, alignFrame);
436 if (alternates.containsKey(service.getName()))
438 atpoint.add(hitm = new JMenu(
439 MessageManager.getString("label.switch_server")));
440 hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
441 MessageManager.getString("label.choose_jabaws_server")));
442 for (final Jws2Instance sv : alternates.get(service.getName()))
445 hitm.add(itm = new JMenuItem(sv.getHostURL()));
446 itm.setForeground(Color.blue);
447 itm.addActionListener(new ActionListener()
451 public void actionPerformed(ActionEvent arg0)
453 new Thread(new Runnable()
458 setPreferredServiceFor(alignFrame, sv.getName(),
459 sv.getServiceType(), sv);
460 changeSupport.firePropertyChange("services",
461 new Vector<Jws2Instance>(), services);
473 * add services using the Java 2.5/2.6/2.7 system which optionally creates
474 * submenus to index by host and service program type
476 private void addEnumeratedServices(final JMenu jws2al,
477 final AlignFrame alignFrame,
478 List<Jws2Instance> enumerableServices)
480 boolean byhost = Cache.getDefault("WSMENU_BYHOST", false),
481 bytype = Cache.getDefault("WSMENU_BYTYPE", false);
483 * eventually, JWS2 services will appear under the same align/etc submenus.
484 * for moment we keep them separate.
488 List<String> hostLabels = new ArrayList<>();
489 Hashtable<String, String> lasthostFor = new Hashtable<>();
490 Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<>();
491 ArrayList<String> hostlist = new ArrayList<>();
492 for (Jws2Instance service : enumerableServices)
494 ArrayList<Jws2Instance> hostservices = hosts
495 .get(service.getHostURL());
496 if (hostservices == null)
498 hosts.put(service.getHostURL(),
499 hostservices = new ArrayList<>());
500 hostlist.add(service.getHostURL());
502 hostservices.add(service);
504 // now add hosts in order of the given array
505 for (String host : hostlist)
507 Jws2Instance orderedsvcs[] = hosts.get(host)
508 .toArray(new Jws2Instance[1]);
509 String sortbytype[] = new String[orderedsvcs.length];
510 for (int i = 0; i < sortbytype.length; i++)
512 sortbytype[i] = orderedsvcs[i].getName();
514 jalview.util.QuickSort.sort(sortbytype, orderedsvcs);
515 for (final Jws2Instance service : orderedsvcs)
517 atpoint = JvSwingUtils.findOrCreateMenu(jws2al,
518 service.getAction());
519 String type = service.getName();
522 atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host);
523 if (atpoint.getToolTipText() == null)
525 atpoint.setToolTipText(MessageManager
526 .formatMessage("label.services_at", new String[]
532 atpoint = JvSwingUtils.findOrCreateMenu(atpoint, type);
533 if (atpoint.getToolTipText() == null)
535 atpoint.setToolTipText(service.getActionText());
538 if (!byhost && !hostLabels.contains(
539 host + service.getName() + service.getActionText()))
540 // !hostLabels.contains(host + (bytype ?
541 // service.serviceType+service.getActionText() : "")))
543 // add a marker indicating where this service is hosted
544 // relies on services from the same host being listed in a
548 if (hostLabels.contains(host))
550 atpoint.addSeparator();
554 hostLabels.add(host);
556 if (lasthostFor.get(service.getAction()) == null
557 || !lasthostFor.get(service.getAction()).equals(host))
559 atpoint.add(hitm = new JMenuItem(host));
560 hitm.setForeground(Color.blue);
561 hitm.addActionListener(new ActionListener()
565 public void actionPerformed(ActionEvent e)
567 Desktop.showUrl(service.getHostURL());
571 JvSwingUtils.wrapTooltip(true, MessageManager
572 .getString("label.open_jabaws_web_page")));
573 lasthostFor.put(service.getAction(), host);
576 host + service.getName() + service.getActionText());
579 service.attachWSMenuEntry(atpoint, alignFrame);
584 public static void main(String[] args)
588 testUrls = new ArrayList<>();
589 for (String url : args)
595 Thread runner = getDiscoverer()
596 .startDiscoverer(new PropertyChangeListener()
600 public void propertyChange(PropertyChangeEvent evt)
602 if (getDiscoverer().services != null)
604 System.out.println("Changesupport: There are now "
605 + getDiscoverer().services.size() + " services");
607 for (Jws2Instance instance : getDiscoverer().services)
609 System.out.println("Service " + i++ + " "
610 + instance.getClass() + "@"
611 + instance.getHostURL()
612 + ": " + instance.getActionText());
618 while (runner.isAlive())
623 } catch (InterruptedException e)
631 } catch (InterruptedException x)
637 * Returns the singleton instance of this class.
641 public static Jws2Discoverer getDiscoverer()
643 if (discoverer == null)
645 discoverer = new Jws2Discoverer();
650 public boolean hasServices()
652 return !running && services != null && services.size() > 0;
655 public boolean isRunning()
660 public void setServiceUrls(List<String> wsUrls)
662 if (wsUrls != null && !wsUrls.isEmpty())
664 StringBuilder urls = new StringBuilder(128);
666 for (String url : wsUrls)
672 Cache.setProperty(JWS2HOSTURLS, urls.toString());
676 Cache.removeProperty(JWS2HOSTURLS);
681 * Returns web service URLs, in the order in which they should be tried (or an
686 public List<String> getServiceUrls()
688 if (testUrls != null)
690 // return test urls, if there are any, instead of touching cache
693 List<String> urls = new ArrayList<>();
695 if (this.preferredUrl != null)
697 urls.add(preferredUrl);
700 String surls = Cache.getDefault(JWS2HOSTURLS, COMPBIO_JABAWS);
703 StringTokenizer st = new StringTokenizer(surls, ",");
704 while (st.hasMoreElements())
709 url = st.nextToken();
711 if (!urls.contains(url))
717 Cache.log.warn("Ignoring duplicate url " + url + " in "
718 + JWS2HOSTURLS + " list");
720 } catch (MalformedURLException ex)
722 Cache.log.warn("Problem whilst trying to make a URL from '"
723 + ((url != null) ? url : "<null>") + "'");
725 "This was probably due to a malformed comma separated list"
726 + " in the " + JWS2HOSTURLS
727 + " entry of $(HOME)/.jalview_properties)");
728 Cache.log.debug("Exception was ", ex);
731 } catch (Exception ex)
733 Cache.log.warn("Error parsing comma separated list of urls in "
734 + JWS2HOSTURLS + " preference.", ex);
739 public Vector<Jws2Instance> getServices()
741 return (services == null) ? new Vector<>()
742 : new Vector<>(services);
746 * test the given URL with the JabaWS test code
751 public static boolean testServiceUrl(URL foo)
755 compbio.ws.client.WSTester
757 { "-h=" + foo.toString() });
758 } catch (Exception e)
762 } catch (OutOfMemoryError e)
775 public boolean restart()
792 * Start a fresh discovery thread and notify the given object when we're
793 * finished. Any known existing threads will be killed before this one is
796 * @param changeSupport2
799 public Thread startDiscoverer(PropertyChangeListener changeSupport2)
807 Thread thr = new Thread(this);
815 addPropertyChangeListener(changeSupport2);
816 Thread thr = new Thread(this);
822 * @return the invalidServiceUrls
824 public Vector<String> getInvalidServiceUrls()
826 return invalidServiceUrls;
830 * @return the urlsWithoutServices
832 public Vector<String> getUrlsWithoutServices()
834 return urlsWithoutServices;
838 * add an 'empty' JABA server to the list. Only servers not already in the
839 * 'bad URL' list will be added to this list.
843 public synchronized void addUrlwithnoservices(String jwsservers)
845 if (urlsWithoutServices == null)
847 urlsWithoutServices = new Vector<>();
850 if ((invalidServiceUrls == null
851 || !invalidServiceUrls.contains(jwsservers))
852 && !urlsWithoutServices.contains(jwsservers))
854 urlsWithoutServices.add(jwsservers);
859 * add a bad URL to the list
863 public synchronized void addInvalidServiceUrl(String jwsservers)
865 if (invalidServiceUrls == null)
867 invalidServiceUrls = new Vector<>();
869 if (!invalidServiceUrls.contains(jwsservers))
871 invalidServiceUrls.add(jwsservers);
877 * @return a human readable report of any problems with the service URLs used
880 public String getErrorMessages()
882 if (!isRunning() && !isAborted())
884 StringBuffer ermsg = new StringBuffer();
885 boolean list = false;
886 if (getInvalidServiceUrls() != null
887 && getInvalidServiceUrls().size() > 0)
889 ermsg.append(MessageManager.getString("warn.urls_not_contacted")
891 for (String svcurl : getInvalidServiceUrls())
898 ermsg.append(svcurl);
900 ermsg.append("\n\n");
903 if (getUrlsWithoutServices() != null
904 && getUrlsWithoutServices().size() > 0)
907 MessageManager.getString("warn.urls_no_jaba") + ": \n");
908 for (String svcurl : getUrlsWithoutServices())
915 ermsg.append(svcurl);
919 if (ermsg.length() > 1)
921 return ermsg.toString();
928 public int getServerStatusFor(String url)
930 if (validServiceUrls != null && validServiceUrls.contains(url))
934 if (urlsWithoutServices != null && urlsWithoutServices.contains(url))
938 if (invalidServiceUrls != null && invalidServiceUrls.contains(url))
946 * pick the user's preferred service based on a set of URLs (jaba server
947 * locations) and service URIs (specifying version and service interface
951 * @return null or best match for given uri/ls.
953 public Jws2Instance getPreferredServiceFor(String[] serviceURLs)
955 HashSet<String> urls = new HashSet<>();
956 urls.addAll(Arrays.asList(serviceURLs));
957 Jws2Instance match = null;
958 if (services != null)
960 for (Jws2Instance svc : services)
962 // TODO getNameURI Should return a versioned URI for the service, but
963 // doesn't as of 2.11
964 if (urls.contains(svc.getNameURI()))
968 // for moment we always pick service from server ordered first in
969 // user's preferences
972 if (urls.contains(svc.getUri()))
974 // stop and return - we've matched type URI and URI for service
984 Map<String, Map<String, String>> preferredServiceMap = new HashMap<>();;
987 * get current preferred endpoint of the given Jabaws service, or global
991 * null or a specific alignFrame
993 * Jws2Instance.getName() for service
994 * @return null if no service of this type is available, the preferred service
995 * for the serviceType and af if specified and if defined.
997 public Jws2Instance getPreferredServiceFor(AlignFrame af,
1000 String serviceurl = null;
1001 synchronized (preferredServiceMap)
1003 String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
1004 Map<String, String> prefmap = preferredServiceMap.get(afid);
1005 if (afid.length() > 0 && prefmap == null)
1007 // recover global setting, if any
1008 prefmap = preferredServiceMap.get("");
1010 if (prefmap != null)
1012 serviceurl = prefmap.get(serviceName);
1016 Jws2Instance response = null;
1017 for (Jws2Instance svc : services)
1019 if (svc.getName().equals(serviceName))
1021 if (serviceurl == null || serviceurl.equals(svc.getHostURL()))
1031 public void setPreferredServiceFor(AlignFrame af, String serviceName,
1032 String serviceAction, Jws2Instance selectedServer)
1034 // TODO: pull out and generalise for the selectedServer's attributes
1035 String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
1036 if (preferredServiceMap == null)
1038 preferredServiceMap = new HashMap<>();
1040 Map<String, String> prefmap = preferredServiceMap.get(afid);
1041 if (prefmap == null)
1043 prefmap = new HashMap<>();
1044 preferredServiceMap.put(afid, prefmap);
1046 prefmap.put(serviceName, selectedServer.getHostURL());
1047 prefmap.put(serviceAction, selectedServer.getHostURL());
1050 public void setPreferredServiceFor(String serviceType,
1051 String serviceAction, Jws2Instance selectedServer)
1053 setPreferredServiceFor(null, serviceType, serviceAction,
1058 * Set a URL to try before any others. For use with command-line parameter to
1059 * configure a local Jabaws installation without the need to add to property
1063 * @throws MalformedURLException
1065 public void setPreferredUrl(String value) throws MalformedURLException
1067 if (value != null && value.trim().length() > 0)
1070 preferredUrl = value;