December 2009 - Isis-fish-commits - mailman.cloud.codelutin.com

r2841 - isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher
by chatellier＠users.labs.libre-entreprise.org Dec. 15, 2009

Dec. 15, 2009

Author: chatellier Date: 2009-12-15 14:14:37 +0000 (Tue, 15 Dec 2009) New Revision: 2841 Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java Log: Move log to trace Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java 2009-12-15 14:07:34 UTC (rev 2840) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java 2009-12-15 14:14:37 UTC (rev 2841) @@ -462,8 +462,8 @@ } else { //checkScheduler.schedule(this, date); - if (log.isDebugEnabled()) { - log.debug("Time to check not reached, skip check, " + date + if (log.isTraceEnabled()) { + log.trace("Time to check not reached, skip check, " + date + " < " + now); } }

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r2840 - in isis-fish/trunk: . src/main/java/fr/ifremer/isisfish/simulator/launcher
by chatellier＠users.labs.libre-entreprise.org Dec. 15, 2009

Dec. 15, 2009

Author: chatellier Date: 2009-12-15 14:07:34 +0000 (Tue, 15 Dec 2009) New Revision: 2840 Modified: isis-fish/trunk/changelog.txt isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java Log: Improve suppression deletion algorithm (deletion > check) Reduce monitoring delay. Simulation can be deleted from caparmor even after isis restart. Modified: isis-fish/trunk/changelog.txt =================================================================== --- isis-fish/trunk/changelog.txt 2009-12-15 13:19:01 UTC (rev 2839) +++ isis-fish/trunk/changelog.txt 2009-12-15 14:07:34 UTC (rev 2840) @@ -1,5 +1,6 @@ isis-fish (3.3.0.0) stable; urgency=low + * Improve simulation stopping algorithm (now faster) * Locally save simulation zip to allow simulation restart even afer isis shutdown * In sensitivity analysis, upload only one zip to caparmor for all simulations * Add option to control number of SSH thread to use Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java 2009-12-15 13:19:01 UTC (rev 2839) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java 2009-12-15 14:07:34 UTC (rev 2840) @@ -29,10 +29,10 @@ import java.io.InputStream; import java.io.OutputStream; import java.rmi.RemoteException; -import java.util.Collection; +import java.text.DateFormat; +import java.text.SimpleDateFormat; import java.util.Comparator; import java.util.Date; -import java.util.Iterator; import java.util.LinkedList; import java.util.List; import java.util.Properties; @@ -83,10 +83,15 @@ /** Class logger. */ private static Log log = LogFactory.getLog(SimulationMonitor.class); + /** Simulation start date format. */ + private static final DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss"); + protected static final String PROPERTIES_FILE = "monitoring.properties"; protected static final String PROPERTY_LAUNCHER = "simulation.launcher"; protected static final String PROPERTY_DATE = "simulation.date"; protected static final String PROPERTY_ZIP = "simulation.zip"; + protected static final String PROPERTY_STANDALONE = "simulation.standalone"; + protected static final String PROPERTY_LASTSIMULATION = "simulation.last"; /** Instance. */ protected static SimulationMonitor instance = new SimulationMonitor(); @@ -224,17 +229,13 @@ try { // launcher - String simulationLauncher = propertiesFile - .getProperty(PROPERTY_LAUNCHER); - SimulatorLauncher launcher = (SimulatorLauncher) Class.forName( - simulationLauncher).newInstance(); + String simulationLauncher = propertiesFile.getProperty(PROPERTY_LAUNCHER); + SimulatorLauncher launcher = (SimulatorLauncher) Class.forName(simulationLauncher).newInstance(); // zip (copy to temp in mandatory) String zipFileName = propertiesFile.getProperty(PROPERTY_ZIP); File zipFile = new File(simulationFolder, zipFileName); - // - File tempZipFile = File.createTempFile( - "simulation-" + simulationId, ".zip"); + File tempZipFile = File.createTempFile("simulation-" + simulationId, ".zip"); FileUtils.copyFile(zipFile, tempZipFile); tempZipFile.deleteOnExit(); @@ -246,11 +247,18 @@ // Et il est relance avec un parametre "checkonly" SimulationParameter params = new SimulationParameter(); SimulationControl control = new SimulationControl(simulationId); + SimulationItem item = new SimulationItem(control, params); item.setSimulationZip(tempZipFile); // tempZipFile, important ! + + // set additionnal parameters (null safe, defaut parameter safe) + String standalone = propertiesFile.getProperty(PROPERTY_STANDALONE); + item.setStandaloneSimulation(!"false".equalsIgnoreCase(standalone)); + String lastSimulation = propertiesFile.getProperty(PROPERTY_LASTSIMULATION); + item.setLastSimulation("true".equalsIgnoreCase(lastSimulation)); + SimulationJob job = new SimulationJob(service, item, 0); job.setLauncher(launcher); - service.submitForCheckOnly(job); } catch (ClassNotFoundException e) { if (log.isErrorEnabled()) { @@ -275,6 +283,7 @@ public synchronized void simulationStart(SimulationJob job) { String simulationId = job.getId(); + SimulationItem simulationItem = job.getItem(); File simulationMonitoringFolder = new File(monitorFolder, simulationId); File simulationPropertiesFile = new File(simulationMonitoringFolder, PROPERTIES_FILE); @@ -287,10 +296,11 @@ simulationProperties.setProperty(PROPERTY_LAUNCHER, launcherName); // date - simulationProperties.setProperty(PROPERTY_DATE, launcherName); + String simulationDate = dateFormat.format(new Date()); + simulationProperties.setProperty(PROPERTY_DATE, simulationDate); // zip - File zipFile = job.getItem().getSimulationZip(); + File zipFile = simulationItem.getSimulationZip(); try { // original zip must be keeped outside monitoring folder FileUtils.copyFileToDirectory(zipFile, simulationMonitoringFolder); @@ -301,6 +311,10 @@ } } + // addtionnal infos + simulationProperties.setProperty(PROPERTY_STANDALONE, String.valueOf(simulationItem.isStandaloneSimulation())); + simulationProperties.setProperty(PROPERTY_LASTSIMULATION, String.valueOf(simulationItem.isLastSimulation())); + // save property file OutputStream out = null; try { @@ -385,25 +399,22 @@ } /** - * Wait one second, and check for first + * Wait a little time, and check for first * simulation progression, if first simulation time * is reached. */ protected void waitAndCheckProgression() { + // wait a minimum time + // 1s is to long to stop 1000 simulations try { - Thread.sleep(1000); + Thread.sleep(10); } catch (InterruptedException e) { if (log.isErrorEnabled()) { log.error("Monitor thread has been interrupted", e); } } - // log - if (log.isDebugEnabled()) { - log.debug("Simulation monitor wake up"); - } - // take first job in map if (!checkSet.isEmpty()) { SimpleEntry<Date, SimulationJob> firstEntry = checkSet.first(); @@ -482,24 +493,25 @@ // update try { - launcher.updateControl(service, control); - - // by default, Progress = ProgressMax = 0 - // WARNING this condition is VERY important - // and set by end of - // fr.ifremer.isisfish.simulator.launcher.InProcessSimulatorLauncher#localSimulateSameThread(SimulationControl, SimulationStorage) - - // FIXME check SimulationStorage.exists(control.getId()) condition - if ((control.getProgress() > 0 - && control.getProgress() >= control.getProgressMax() && SimulationStorage - .exists(control.getId()))) { - simulationEnded = true; - } - if (control.isStopSimulationRequest()) { - launcher.simulationStopRequest(job); // to release one resource + launcher.simulationStopRequest(job); simulationEnded = true; } + else { + launcher.updateControl(service, control); + + // by default, Progress = ProgressMax = 0 + // WARNING this condition is VERY important + // and set by end of + // fr.ifremer.isisfish.simulator.launcher.InProcessSimulatorLauncher#localSimulateSameThread(SimulationControl, SimulationStorage) + + // FIXME check SimulationStorage.exists(control.getId()) condition + if ((control.getProgress() > 0 + && control.getProgress() >= control.getProgressMax() && SimulationStorage + .exists(control.getId()))) { + simulationEnded = true; + } + } } catch (RemoteException e) { if (log.isErrorEnabled()) { log.error("Progression thread update error", e); @@ -710,25 +722,4 @@ return simulationStorageForAnalyze; } - - /** - * Convertit une collection de string, en une chaine - * séparée par des ",". - * - * @param collection collection to convert - * @return string - */ - protected static String collectionToString(Collection<String> collection) { - String str = ""; - - Iterator<String> it = collection.iterator(); - while (it.hasNext()) { - str += it.next(); - if (it.hasNext()) { - str += ","; - } - } - - return str; - } } // SimulationMonitor

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r2839 - isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher
by chatellier＠users.labs.libre-entreprise.org Dec. 15, 2009

Dec. 15, 2009

Author: chatellier Date: 2009-12-15 13:19:01 +0000 (Tue, 15 Dec 2009) New Revision: 2839 Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java Log: Fix simulation stop request on caparmor (upload with short id, stopped as well) Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java 2009-12-15 12:47:20 UTC (rev 2838) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java 2009-12-15 13:19:01 UTC (rev 2839) @@ -231,8 +231,10 @@ // multi jobs has been started with last one // must be killed with last one too if (simulationItem.isLastSimulation()) { + String simulationid = simulationItem.getControl().getId(); + String shortSimulationId = simulationid.substring(0, simulationid.lastIndexOf('_')); try { - sendStopSimulationRequest(sshSession, simulationItem.getControl().getId()); + sendStopSimulationRequest(sshSession, shortSimulationId); } catch (SSHException e) { throw new RemoteException("Can't connect", e); }

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r2838 - in isis-fish/trunk/src/main: java/fr/ifremer/isisfish/ui/config resources/i18n
by chatellier＠users.labs.libre-entreprise.org Dec. 15, 2009

Dec. 15, 2009

Author: chatellier Date: 2009-12-15 12:47:20 +0000 (Tue, 15 Dec 2009) New Revision: 2838 Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigAction.java isis-fish/trunk/src/main/resources/i18n/isis-fish-en_GB.properties isis-fish/trunk/src/main/resources/i18n/isis-fish-fr_FR.properties Log: Fix free space user confirmation message Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigAction.java =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigAction.java 2009-12-15 11:47:40 UTC (rev 2837) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigAction.java 2009-12-15 12:47:20 UTC (rev 2838) @@ -384,7 +384,7 @@ throw new IllegalArgumentException("Can't delete directory : " + path); } - int response = JOptionPane.showConfirmDialog(configUI, _("isisfish.simulator.ssh.configuration.freespace.confirmdelete", currentSSHDatapath), + int response = JOptionPane.showConfirmDialog(configUI, _("isisfish.simulator.ssh.configuration.freespace.confirmdelete", path), _("isisfish.common.confirm"), JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE); if (response == JOptionPane.YES_OPTION) { Modified: isis-fish/trunk/src/main/resources/i18n/isis-fish-en_GB.properties =================================================================== --- isis-fish/trunk/src/main/resources/i18n/isis-fish-en_GB.properties 2009-12-15 11:47:40 UTC (rev 2837) +++ isis-fish/trunk/src/main/resources/i18n/isis-fish-en_GB.properties 2009-12-15 12:47:20 UTC (rev 2838) @@ -939,7 +939,7 @@ isisfish.simulator.ssh.configuration.connectionok=Connection successfull isisfish.simulator.ssh.configuration.environment=Caparmor configuration isisfish.simulator.ssh.configuration.freespace=Used space disk \: -isisfish.simulator.ssh.configuration.freespace.confirmdelete=Warning, deleting the contents of file '%s' is irreversible.\nDo you confirm the deletion of contents ? +isisfish.simulator.ssh.configuration.freespace.confirmdelete=Warning, deleting folder '%s' is irreversible.\nDo you confirm the deletion of contents ? isisfish.simulator.ssh.configuration.freespace.label=Size of %s \: %s isisfish.simulator.ssh.configuration.invalidpassphrase=Invalid passphrase isisfish.simulator.ssh.configuration.keygenerate=Generate Modified: isis-fish/trunk/src/main/resources/i18n/isis-fish-fr_FR.properties =================================================================== --- isis-fish/trunk/src/main/resources/i18n/isis-fish-fr_FR.properties 2009-12-15 11:47:40 UTC (rev 2837) +++ isis-fish/trunk/src/main/resources/i18n/isis-fish-fr_FR.properties 2009-12-15 12:47:20 UTC (rev 2838) @@ -939,7 +939,7 @@ isisfish.simulator.ssh.configuration.connectionok=Connect\u00E9 avec succ\u00E8s isisfish.simulator.ssh.configuration.environment=Configuration sur Caparmor isisfish.simulator.ssh.configuration.freespace=Espace disque utilis\u00E9 \: -isisfish.simulator.ssh.configuration.freespace.confirmdelete=Attention, la suppression du contenu du dossier '%s' est irr\u00E9versible.\nConfirmez-vous la suppression de son contenu ? +isisfish.simulator.ssh.configuration.freespace.confirmdelete=Attention, la suppression du dossier '%s' est irr\u00E9versible.\nConfirmez-vous la suppression de son contenu ? isisfish.simulator.ssh.configuration.freespace.label=Taille de %s \: %s isisfish.simulator.ssh.configuration.invalidpassphrase=Passphrase invalide isisfish.simulator.ssh.configuration.keygenerate=G\u00E9n\u00E9rer

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r2837 - isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher
by chatellier＠users.labs.libre-entreprise.org Dec. 15, 2009

Dec. 15, 2009

Author: chatellier Date: 2009-12-15 11:47:40 +0000 (Tue, 15 Dec 2009) New Revision: 2837 Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java Log: Upload multijob script with small simulation id name Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java 2009-12-15 11:25:57 UTC (rev 2836) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java 2009-12-15 11:47:40 UTC (rev 2837) @@ -1019,7 +1019,7 @@ // multiples jobs simulation File simulationPSBScript = getLaunchSimulationScriptFile(shortSimulationId, simulationRemoteZipPath, simulationItem.isStandaloneSimulationZip(), remoteResultZip, simulationPreScriptPath, true); - String scriptRemotePath = uploadSimulationScript(sshSession, simulationid, simulationPSBScript); + String scriptRemotePath = uploadSimulationScript(sshSession, shortSimulationId, simulationPSBScript); // prescript uploaded, delete simulationPSBScript.delete();

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r2836 - isis-fish/trunk
by chatellier＠users.labs.libre-entreprise.org Dec. 15, 2009

Dec. 15, 2009

Author: chatellier Date: 2009-12-15 11:25:57 +0000 (Tue, 15 Dec 2009) New Revision: 2836 Modified: isis-fish/trunk/pom.xml Log: Set snapshot name same as copy dependency name ! Modified: isis-fish/trunk/pom.xml =================================================================== --- isis-fish/trunk/pom.xml 2009-12-15 10:53:09 UTC (rev 2835) +++ isis-fish/trunk/pom.xml 2009-12-15 11:25:57 UTC (rev 2836) @@ -457,6 +457,7 @@ <addClasspath>true</addClasspath> <mainClass>fr.ifremer.isisfish.IsisFish</mainClass> <classpathPrefix>lib/</classpathPrefix> + <useUniqueVersions>false</useUniqueVersions> </manifest> </archive> </configuration>

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r2835 - isis-fish/trunk/src/main/assembly
by chatellier＠users.labs.libre-entreprise.org Dec. 15, 2009

Dec. 15, 2009

Author: chatellier Date: 2009-12-15 10:53:09 +0000 (Tue, 15 Dec 2009) New Revision: 2835 Modified: isis-fish/trunk/src/main/assembly/bin.xml Log: Update assembly for maven3 (non hack code works only only in maven3) Modified: isis-fish/trunk/src/main/assembly/bin.xml =================================================================== --- isis-fish/trunk/src/main/assembly/bin.xml 2009-12-15 10:07:24 UTC (rev 2834) +++ isis-fish/trunk/src/main/assembly/bin.xml 2009-12-15 10:53:09 UTC (rev 2835) @@ -8,9 +8,6 @@

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r2834 - isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity
by jcouteau＠users.labs.libre-entreprise.org Dec. 15, 2009

Dec. 15, 2009

Author: jcouteau Date: 2009-12-15 10:07:24 +0000 (Tue, 15 Dec 2009) New Revision: 2834 Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java Log: clean code using new nuiton-j2r features Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java 2009-12-14 18:24:08 UTC (rev 2833) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java 2009-12-15 10:07:24 UTC (rev 2834) @@ -164,34 +164,26 @@ REngine engine = new RProxy(); //clear the engine (to be sure it's empty) - log.info("rm(list=ls())"); - engine.voidEval("rm(list=ls())"); + engine.clearSession(); Rcall = String.format(nomFacteur, factorNames); - log.info(Rcall); engine.voidEval(Rcall); Rcall = String.format(nominal, nominalValues); - log.info(Rcall); engine.voidEval(Rcall); Rcall = String.format(continu, continuValues); - log.info(Rcall); engine.voidEval(Rcall); Rcall = String.format(binf, binfValues); - log.info(Rcall); engine.voidEval(Rcall); Rcall = String.format(bsup, bsupValues); - log.info(Rcall); engine.voidEval(Rcall); - log.info(isisfactors); engine.voidEval(isisfactors); Rcall = String.format(attribute, "nomModel", "isis-fish-externeR"); - log.info(Rcall); engine.voidEval(Rcall); for (int i = 0; i < factors.size(); i++) { @@ -210,23 +202,14 @@ Rcall = String.format(attribute, factor.getName(), attributeValues); - log.info(Rcall); engine.voidEval(Rcall); } } - //Set working directory to save the Isis R session - log.info("setwd(\"" - + outputdirectory.getParent().replaceAll("\\\\", "/") - + "\")"); - engine.voidEval("setwd(\"" - + outputdirectory.getParent().replaceAll("\\\\", "/") - + "\")"); + //Save the Isis R session + engine.saveRData(outputdirectory.getParentFile(), + outputdirectory.getName()); - log.info("save.image(file=\"" + outputdirectory.getName() + ".RData\")"); - engine.voidEval("save.image(file=\"" + outputdirectory.getName() - + ".RData\")"); - } catch (RException eee) { if (log.isErrorEnabled()) { log.error("R evaluation failed", eee);

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r2833 - isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/result
by chatellier＠users.labs.libre-entreprise.org Dec. 14, 2009

Dec. 14, 2009

Author: chatellier Date: 2009-12-14 18:24:08 +0000 (Mon, 14 Dec 2009) New Revision: 2833 Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/result/DataResult.java isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/result/ResultEdit.java Log: Remove System.out. Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/result/DataResult.java =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/result/DataResult.java 2009-12-14 18:12:26 UTC (rev 2832) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/result/DataResult.java 2009-12-14 18:24:08 UTC (rev 2833) @@ -57,7 +57,6 @@ * Affiche le titre de la matrice */ public void loadDescription(){ - System.out.println(getMatrix().getName()); getDescriptionLabel().setText(getMatrix().getName()); } Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/result/ResultEdit.java =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/result/ResultEdit.java 2009-12-14 18:12:26 UTC (rev 2832) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/result/ResultEdit.java 2009-12-14 18:24:08 UTC (rev 2833) @@ -259,7 +259,7 @@ for(Iterator i=resultManager.getResultName().iterator(); i.hasNext();){ String name = (String)i.next(); try { - System.out.println(name); + if (name.startsWith(ABONDANCE_STRING)){ MatrixND mat1 = resultManager.getMatrix(new Date(0), name, tx); mat1 = mat1.sumOverDim(0);

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r2832 - isis-fish/trunk
by chatellier＠users.labs.libre-entreprise.org Dec. 14, 2009

Dec. 14, 2009

Author: chatellier Date: 2009-12-14 18:12:26 +0000 (Mon, 14 Dec 2009) New Revision: 2832 Modified: isis-fish/trunk/pom.xml Log: Switch to stable release Modified: isis-fish/trunk/pom.xml =================================================================== --- isis-fish/trunk/pom.xml 2009-12-14 16:26:56 UTC (rev 2831) +++ isis-fish/trunk/pom.xml 2009-12-14 18:12:26 UTC (rev 2832) @@ -413,8 +413,8 @@ <properties>  <jaxx.version>1.7.1</jaxx.version> - <eugene.version>2.0.0-beta-SNAPSHOT</eugene.version> - <topia.version>2.3.0-beta-SNAPSHOT</topia.version> + <eugene.version>2.0.0-beta-1</eugene.version> + <topia.version>2.3.0-beta-1</topia.version> <nuiton-utils.version>1.1.2-SNAPSHOT</nuiton-utils.version> <nuiton-i18n.version>1.0.1</nuiton-i18n.version> <nuiton-widgets.version>1.0.1-SNAPSHOT</nuiton-widgets.version>

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