1 package uk.ac.vamsas.test;
3 import uk.ac.vamsas.client.*;
4 import uk.ac.vamsas.client.picking.IMessageHandler;
5 import uk.ac.vamsas.client.picking.IPickManager;
6 import uk.ac.vamsas.client.picking.Message;
7 import uk.ac.vamsas.objects.core.VAMSAS;
8 import uk.ac.vamsas.test.objects.Core;
10 import java.awt.Event;
11 import java.beans.PropertyChangeEvent;
12 import java.beans.PropertyChangeListener;
14 import java.io.IOException;
15 import java.util.Vector;
18 * Toy vamsas command line client application demonstrating the API.
19 * Currently runs with one argument: ExampleApplication.main(new String("watch"))
20 * Test: Start up at least two of these processes independently and they will
21 * successively modify and handle update events from the document model.
23 * Behaviour of each client:
24 * Event handlers are registered for documentUpdate.
25 * - every document update:
26 * * the vamsas document will be dumped to standard out using uk.ac.vamsas.test.simpleclient.ArchiveReports
27 * * if there are more than 4 vamsas roots, the first sequence in the first alignment of the first dataset of the second vamsas root will be appended with a single gap character and then written back to the session document.
28 * A pick thread is started, which sends random CUSTOM pick events every so often (tuning: flooding the pick channel seems to affect the behaviour of other vamsasClient threads, suggesting some object lock contention).
29 * A new vamsas root generated from uk.ac.vamsas.test.objects.Core.getDemoVamsas is added to the document.
30 * Then a while loop waits around for events until shutdown:
31 * - currently it will shutdown after 9 updates (totalUpdates)
32 * - an update will be made after every other update that is detected.
34 * Status: PickManager now shuts down correctly. Serial updates for two instances work correctly and are detected under j1.4 (need to test in 1.5 and 1.6).
37 * appData get/set methods
39 * TODO: verify and test pickManager and interaction
40 * between it and other session events
42 * TODO: add more session interaction events
44 * TODO: test client add/leave events - currently library generates exceptions for sessionlist and clientlist modifications.
49 public class ExampleApplication
51 private ClientHandle app;
53 private UserHandle user; // TODO: make this something defined by the
56 private IClientFactory clientfactory;
58 private IClient vorbaclient;
60 private byte[] mydata;
62 private Vector vamsasObjects;
64 private boolean isUpdated = false;
66 private boolean isShuttingdown = false;
68 private boolean isFinalizing = false;
69 private int totalUpdates = 9;
70 private void processVamsasDocument(IClientDocument doc)
72 if (doc.getVamsasRoots().length<4) {
73 doc.addVamsasRoot(Core.getDemoVamsas());
76 uk.ac.vamsas.objects.core.DataSet ds = doc.getVamsasRoots()[1].getDataSet(0);
77 uk.ac.vamsas.objects.core.AlignmentSequence alsq = ds.getAlignment(0).getAlignmentSequence(0);
78 System.out.println("Modifying Sequence:\n"+alsq.hashCode());
79 alsq.setSequence(alsq.getSequence()+ds.getAlignment(0).getGapChar());
80 System.out.println("Modifying Sequence:\n"+alsq.hashCode());
81 System.out.println("Modified Sequence:\n"+alsq.getSequence());
82 doc.setVamsasRoots(doc.getVamsasRoots());
83 } catch (Exception ee) {
87 vorbaclient.updateDocument(doc);
88 // merge vamsasObjects with vamsas objects in document
89 // get this apps 'mydata' if it hasn't got it already.
90 // .. access this application's 'public' mydata' if there is any.
93 private void addHandlers(IClient avorbaclient)
95 // make a non-volatile reference to the client instance.
96 final IClient vorbaclient = avorbaclient;
97 // register update handler
98 vorbaclient.addDocumentUpdateHandler(new PropertyChangeListener() {
99 public void propertyChange(PropertyChangeEvent evt)
101 System.out.println("Vamsas document update for "
102 + evt.getPropertyName() + ": " + evt.getOldValue()
103 + " to " + evt.getNewValue());
104 // merge new data into ours.
105 // example - output doc
108 IClientDocument cdoc = vorbaclient.getClientDocument();
109 uk.ac.vamsas.test.simpleclient.ArchiveReports.rootReport(
110 cdoc.getVamsasRoots(), true, System.out);
113 if (cdoc.getVamsasRoots().length>2) {
114 uk.ac.vamsas.objects.core.DataSet ds = cdoc.getVamsasRoots()[1].getDataSet(0);
115 uk.ac.vamsas.objects.core.AlignmentSequence alsq = ds.getAlignment(0).getAlignmentSequence(0);
116 if (alsq.isUpdated())
117 System.out.println("Seqeuence was updated since last time.");
118 alsq.setSequence(alsq.getSequence()+ds.getAlignment(0).getGapChar());
119 System.out.println("Newly Modified Sequence:\n"+alsq.getSequence());
120 cdoc.setVamsasRoots(cdoc.getVamsasRoots());
122 } catch (Exception ee) {
123 System.err.println("Exception whilst updating :");
124 ee.printStackTrace(System.err);
126 vorbaclient.updateDocument(cdoc);
131 .println("Exception whilst dumping document tree after an update.");
132 e.printStackTrace(System.err);
134 isUpdated = true; // tell main thread to reflect change...
137 // register close handler
138 vorbaclient.addVorbaEventHandler(Events.DOCUMENT_REQUESTTOCLOSE,
139 new PropertyChangeListener() {
140 public void propertyChange(PropertyChangeEvent evt)
143 .println("Received request to close vamsas document.");
144 // ask user for a filename to save it to.
145 // Then pass it to the vorba object...
146 vorbaclient.storeDocument(new java.io.File(
151 // register some more handlers to monitor the session :
153 vorbaclient.addVorbaEventHandler(Events.CLIENT_CREATION,
154 new PropertyChangeListener() {
155 public void propertyChange(PropertyChangeEvent evt)
157 System.out.println("New Vamsas client for "
158 + evt.getPropertyName() + ": "
159 + evt.getOldValue() + " to "
160 + evt.getNewValue());
161 // tell app add new client to its list of clients.
164 vorbaclient.addVorbaEventHandler(Events.CLIENT_FINALIZATION,
165 new PropertyChangeListener() {
166 public void propertyChange(PropertyChangeEvent evt)
168 System.out.println("Vamsas client finalizing for "
169 + evt.getPropertyName() + ": "
170 + evt.getOldValue() + " to "
171 + evt.getNewValue());
172 // tell app to update its list of clients to communicate
176 vorbaclient.addVorbaEventHandler(Events.SESSION_SHUTDOWN,
177 new PropertyChangeListener() {
178 public void propertyChange(PropertyChangeEvent evt)
180 System.out.println("Session " + evt.getPropertyName()
181 + " is shutting down.");
182 // tell app to finalize its session data before
186 vorbaclient.addVorbaEventHandler(Events.DOCUMENT_FINALIZEAPPDATA,
187 new PropertyChangeListener() {
188 public void propertyChange(PropertyChangeEvent evt)
191 .println("Application received a DOCUMENT_FINALIZEAPPDATA event.");
192 // tell app to finalize its session data prior to the
193 // storage of the current session as an archive.
199 public String Usage = "ExampleApplication :/n [-arena <vamsasFileDirectory>][-session <vamsasSessionURN>] <action> [+<arguments>]\n"
200 + "<action> is one of :\n\tsave,update,close,watch";
203 String importFile=null;
204 String outputFile=null;
205 private boolean parseArgs(String args[])
207 if (args.length == 0)
212 boolean parsed=false;
213 while (!parsed && cpos<args.length)
215 if (args[cpos].toLowerCase().equals("load") && cpos+1<args.length)
217 importFile=args[cpos+1];
221 if (args[cpos].toLowerCase().equals("save") && cpos+1<args.length)
223 outputFile=args[cpos+1];
227 // default behaviour - if not anything else its probably a session urn
228 if (!args[cpos].toLowerCase().equals("watch"))
237 class ExamplePicker extends Thread
241 public IPickManager pm = null;
243 ExamplePicker(String me, IPickManager pm)
254 try { Thread.sleep(1000 + (long) Math.random() * 10000); }
255 catch (Exception e) {}
259 pm.sendMessage(new uk.ac.vamsas.client.picking.CustomMessage("Message " + mcount++ + " from " + me));
266 public void runMe(String[] args)
268 if (!parseArgs(args))
270 System.err.print(Usage);
272 // get IClientFactory
275 clientfactory = new uk.ac.vamsas.client.simpleclient.SimpleClientFactory();
277 catch (IOException e)
279 System.err.println(e + "\n" + Usage);
283 // get an Iclient with session data
284 app = new ClientHandle("uk.ac.vamsas.test.ExampleApplication", "0.1");
285 user = new UserHandle("arnolduser", "deathsdoor");
290 System.out.println("Connecting to "+sess);
291 vorbaclient = clientfactory.getIClient(app, user, sess);
295 vorbaclient = clientfactory.getIClient(app, user);
298 catch (NoDefaultSessionException e)
301 .println("There appear to be several sessions to choose from :");
302 String[] sessions = clientfactory.getCurrentSessions();
303 for (int s = 0; s < sessions.length; s++)
304 System.err.println(sessions[s]);
307 addHandlers(vorbaclient);
310 vorbaclient.joinSession();
314 se.printStackTrace();
315 System.err.println(se + " when joining session.\n" + Usage);
318 // register an update listener and a close listener.
319 // import any data if requested to
320 if (importFile!=null)
322 File vfile = new File(importFile);
325 vorbaclient.importDocument(vfile);
329 System.err.println("Failed to import file "+importFile);
330 System.err.println("Exception received was "+e);
331 e.printStackTrace(System.err);
335 // Write out any data if requested to
336 if (outputFile!=null)
338 File vfile = new File(outputFile);
341 vorbaclient.storeDocument(vfile);
345 System.err.println("Failed to export session as file "+outputFile);
346 System.err.println("Exception received was "+e);
347 e.printStackTrace(System.err);
353 IClientDocument cdoc = vorbaclient.getClientDocument();
354 processVamsasDocument(cdoc);
359 .println("Unexpected exception when retrieving the client document for the first time!");
360 e.printStackTrace(System.err);
364 ExamplePicker picker = new ExamplePicker(vorbaclient.getClientHandle()
365 .getClientUrn(), vorbaclient.getPickManager());
368 if (picker.pm!=null) {
369 picker.pm.registerMessageHandler(new IMessageHandler() {
371 public void handleMessage(Message message)
374 .println("Received |" + message.getRawMessage() + "|");
379 while (!isShuttingdown && update < totalUpdates)
381 // do something with data
382 // , update document, or something.
386 System.out.println("Update handler called " + (++update)
389 .println("******************************************");
390 isUpdated = false; // TODO: saner update det method.
395 IClientDocument cdoc = vorbaclient.getClientDocument();
396 processVamsasDocument(cdoc);
401 .println("Error when updating document after an even numbered update.");
402 e.printStackTrace(System.err);
407 try { Thread.sleep(50); }
408 catch (Exception e) {}
411 System.out.println("Finalizing.");
412 // call finalizeClient
413 vorbaclient.finalizeClient();
414 System.out.println("Shutting down picker.");
416 while (picker.isAlive())
418 System.out.println("Waiting for picker to die...");
429 // { meanwhile, eventHandlers are called to do any saves if need be }
430 // and all registered listeners will be deregistered to avoid deadlock.
433 System.out.println("Byee!");
435 public static void main(String[] args)
437 ExampleApplication example = new ExampleApplication();