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r4019 - in trunk/src/main/java/fr/ifremer/isisfish: simulator/sensitivity simulator/sensitivity/domain ui/sensitivity/wizard
by echatellier＠users.forge.codelutin.com June 17, 2014

June 17, 2014

Author: echatellier Date: 2014-06-17 14:34:23 +0200 (Tue, 17 Jun 2014) New Revision: 4019 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4019 Log: fixes #5245: R?\195?\169introduire la possibilit?\195?\169 de d?\195?\169finir des facteurs continus sur des matrices Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityUtils.java trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/ContinuousDistributionPanel.java trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/SensitivityWizardHandler.java Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityUtils.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityUtils.java 2014-06-17 09:02:25 UTC (rev 4018) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityUtils.java 2014-06-17 12:34:23 UTC (rev 4019) @@ -30,6 +30,7 @@ import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +import org.nuiton.math.matrix.MatrixND; import fr.ifremer.isisfish.entities.Equation; import fr.ifremer.isisfish.types.RangeOfValues; @@ -134,6 +135,8 @@ result = true; } else if (value instanceof Equation) { result = true; + } else if (value instanceof MatrixND) { + result = true; } else if (value instanceof RangeOfValues) { RangeOfValues rangeOfValues = (RangeOfValues)value; if (rangeOfValues.getType().equals("Float")) { Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java 2014-06-17 09:02:25 UTC (rev 4018) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java 2014-06-17 12:34:23 UTC (rev 4019) @@ -35,6 +35,7 @@ import org.apache.commons.beanutils.MethodUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +import org.nuiton.math.matrix.MatrixND; import fr.ifremer.isisfish.IsisFishRuntimeException; import fr.ifremer.isisfish.simulator.sensitivity.Distribution; @@ -178,19 +179,19 @@ args.add(identifier); // build distribution param args list - Class distClass = distribution.getDistClass(); + // QUNIFPC est un cas particulier dans toutes les distributions possibles if (distribution == Distribution.QUNIFPC) { // special management : % to min/max Object reference = distributionParameters.get(Distribution.QUNIFPC.getDistibutionParams()[0].getName()); double coef = (Double)distributionParameters.get(Distribution.QUNIFPC.getDistibutionParams()[1].getName()); - double ref = (Double)reference; - args.add(ref * (1.0 - coef)); // min - args.add(ref * (1.0 + coef)); // max - } else if (distribution == Distribution.QUNIFMM) { - Object min = distributionParameters.get(Distribution.QUNIFMM.getDistibutionParams()[0].getName()); - args.add(min); - Object max = distributionParameters.get(Distribution.QUNIFMM.getDistibutionParams()[1].getName()); - args.add(max); + if (reference instanceof MatrixND) { + args.add(1.0 - coef); // min + args.add(1.0 + coef); // max + } else { + double ref = (Double)reference; + args.add(ref * (1.0 - coef)); // min + args.add(ref * (1.0 + coef)); // max + } } else { for (DistributionParam param : distribution.getDistibutionParams()) { String name = param.getName(); @@ -199,11 +200,13 @@ } } - // add default value for lower.tail = TRUE, log.p = FALSE + // add default value for lower.tail = TRUE args.add(true); + // add default value forlog.p = FALSE args.add(false); // invoke quantile method + Class distClass = distribution.getDistClass(); Object result = null; try { result = MethodUtils.invokeStaticMethod(distClass, "quantile", args.toArray()); @@ -213,6 +216,14 @@ } } + // pour les matrices, on retourne la matrice multipliée par la valeur données par R + if (distribution == Distribution.QUNIFPC) { + Object reference = distributionParameters.get(Distribution.QUNIFPC.getDistibutionParams()[0].getName()); + if (reference instanceof MatrixND) { + MatrixND ref = ((MatrixND)reference).copy(); + result = ref.mults((Double)result); + } + } return result; } Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/ContinuousDistributionPanel.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/ContinuousDistributionPanel.java 2014-06-17 09:02:25 UTC (rev 4018) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/ContinuousDistributionPanel.java 2014-06-17 12:34:23 UTC (rev 4019) @@ -44,6 +44,8 @@ import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +import org.nuiton.math.matrix.MatrixND; +import org.nuiton.math.matrix.gui.MatrixPanelEditor; import fr.ifremer.isisfish.simulator.sensitivity.Distribution; import fr.ifremer.isisfish.simulator.sensitivity.Distribution.DistributionParam; @@ -89,8 +91,16 @@ GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0, 0, 0, 0), 0, 0)); + // values possibility depending on input type + Distribution[] values; + if (originalValue instanceof MatrixND) { + values = new Distribution[]{Distribution.QUNIFPC}; + } else { + values = Distribution.values(); + } + // combobox - distributionCombo = new JComboBox<Distribution>(Distribution.values()); + distributionCombo = new JComboBox<Distribution>(values); // important : for setSelectedItem to fire event distributionCombo.setSelectedItem(null); distributionCombo.addItemListener(this); @@ -128,7 +138,11 @@ if (value != null) { JComponent comp = paramComponents.get(paramComponentIndex); - ((JTextComponent)comp).setText(value.toString()); + if (comp instanceof MatrixPanelEditor) { + ((MatrixPanelEditor)comp).setMatrix((MatrixND)value); + } else { + ((JTextComponent)comp).setText(value.toString()); + } } else { if (log.isWarnEnabled()) { log.warn("Param " + param.getName() + " not found during init"); @@ -180,16 +194,28 @@ JComponent paramField = getParamField(param); paramField.setToolTipText(param.getDescription()); - // rendu simple - dynamicPanel.add(paramLabel, new GridBagConstraints(0, index, 1, 1, 0, 0, - GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, - new Insets(0, 0, 0, 0), 0, 0)); + // rendu étendu pour les matrix panels + if (paramField instanceof MatrixPanelEditor) { + dynamicPanel.add(paramLabel, new GridBagConstraints(0, index, 2, 1, 0, 0, + GridBagConstraints.NORTHWEST, GridBagConstraints.HORIZONTAL, + new Insets(0, 0, 0, 0), 0, 0)); + index++; + dynamicPanel.add(paramField, new GridBagConstraints(0, index, 2, 1, 1, 1, + GridBagConstraints.NORTH, GridBagConstraints.BOTH, + new Insets(0, 0, 0, 0), 0, 0)); + index++; + } else { + // rendu simple + dynamicPanel.add(paramLabel, new GridBagConstraints(0, index, 1, 1, 0, 0, + GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, + new Insets(0, 0, 0, 0), 0, 0)); + + dynamicPanel.add(paramField, new GridBagConstraints(1, index, 1, 1, 1, 0, + GridBagConstraints.NORTH, GridBagConstraints.HORIZONTAL, + new Insets(0, 0, 0, 0), 0, 0)); + index++; + } - dynamicPanel.add(paramField, new GridBagConstraints(1, index, 1, 1, 1, 0, - GridBagConstraints.NORTH, GridBagConstraints.HORIZONTAL, - new Insets(0, 0, 0, 0), 0, 0)); - index++; - paramComponents.add(paramField); } @@ -211,7 +237,12 @@ JComponent result; if (param.isOriginalValue()) { - result = new JTextField(originalValue.toString()); + if (originalValue instanceof MatrixND) { + result = new MatrixPanelEditor(); + ((MatrixPanelEditor)result).setMatrix((MatrixND)originalValue); + } else { + result = new JTextField(originalValue.toString()); + } } else { result = new JTextField(); } @@ -250,9 +281,13 @@ for (DistributionParam param : params) { JComponent comp = paramComponents.get(paramComponentIndex); - // XXX echatellier 20131201 : always double type ? - String strValue = ((JTextComponent)comp).getText().trim(); - domain.addDistributionParam(param.getName(), Double.parseDouble(strValue)); + if (comp instanceof MatrixPanelEditor) { + domain.addDistributionParam(param.getName(), ((MatrixPanelEditor)comp).getMatrix()); + } else { + // XXX echatellier 20131201 : always double type ? + String strValue = ((JTextComponent)comp).getText().trim(); + domain.addDistributionParam(param.getName(), Double.parseDouble(strValue)); + } paramComponentIndex++; } Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/SensitivityWizardHandler.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/SensitivityWizardHandler.java 2014-06-17 09:02:25 UTC (rev 4018) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/SensitivityWizardHandler.java 2014-06-17 12:34:23 UTC (rev 4019) @@ -372,6 +372,9 @@ ui.setBeanProperty(property); ui.setBean(bean); result = ui; + } else if (value instanceof MatrixND) { + MatrixND matrix = (MatrixND)value; + result = new ContinuousDistributionPanel(matrix.clone()); } else if (value instanceof TimeUnit) { TimeUnit timeUnit = (TimeUnit)value; //DefaultContinuousPanelUI ui = new DefaultContinuousPanelUI(); @@ -580,6 +583,9 @@ ui.setBeanProperty(property); ui.setBean(entity); result = ui; + } else if (value instanceof MatrixND) { + MatrixND matrix = (MatrixND)value; + result = new ContinuousDistributionPanel(matrix.clone()); } else if (value instanceof TimeUnit) { TimeUnit timeUnit = (TimeUnit)value; //DefaultContinuousPanelUI ui = new DefaultContinuousPanelUI(); @@ -597,7 +603,24 @@ topiaContext.closeContext(); } else { - if (factorPath.startsWith("parameters.rule.")) { + if (factorPath.startsWith("parameters.population.")) { + // la seule facon d'avoir les parametres ici est d'aller + // les chercher dans les parametres de simulation + Pattern pattern = Pattern.compile("^parameters\\.population\\.(\\w+)(\\.(.+)?)$"); + Matcher matcher = pattern.matcher(factorPath); + if (matcher.matches()) { + String populationName = matcher.group(1); + if (log.isDebugEnabled()) { + log.debug("Loading population : " + populationName); + } + TopiaContext topiaContext = getTopiaContext(factorWizardUI); + Population pop = IsisFishDAOHelper.getPopulationDAO(topiaContext).findByName(populationName); + SimulAction action = factorWizardUI.getContextValue(SimulAction.class); + MatrixND N = action.getSimulationParameter().getNumberOf(pop); + result = new ContinuousDistributionPanel(N.clone()); + topiaContext.closeContext(); + } + } else if (factorPath.startsWith("parameters.rule.")) { Pattern pattern = Pattern.compile("^parameters\\.rule\\.(\\d+)\\.parameter\\.(\\w+)(\\..+)?$"); Matcher matcher = pattern.matcher(factorPath); if (matcher.matches()) {

1 0

r4018 - in trunk/src/main: java/fr/ifremer/isisfish/datastore java/fr/ifremer/isisfish/ui/input resources/i18n
by echatellier＠users.forge.codelutin.com June 17, 2014

June 17, 2014

Author: echatellier Date: 2014-06-17 11:02:25 +0200 (Tue, 17 Jun 2014) New Revision: 4018 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4018 Log: Remove import from v2 Removed: trunk/src/main/java/fr/ifremer/isisfish/datastore/update/ Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/input/InputHandler.java trunk/src/main/java/fr/ifremer/isisfish/ui/input/InputUI.jaxx trunk/src/main/resources/i18n/isis-fish_en_GB.properties trunk/src/main/resources/i18n/isis-fish_fr_FR.properties Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/input/InputHandler.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/input/InputHandler.java 2014-06-16 16:04:46 UTC (rev 4017) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/input/InputHandler.java 2014-06-17 09:02:25 UTC (rev 4018) @@ -61,7 +61,6 @@ import fr.ifremer.isisfish.datastore.RegionStorage; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.datastore.StorageException; -import fr.ifremer.isisfish.datastore.update.ImportFromV2; import fr.ifremer.isisfish.entities.Cell; import fr.ifremer.isisfish.entities.FisheryRegion; import fr.ifremer.isisfish.entities.Gear; @@ -314,29 +313,6 @@ } /** - * Importer la region depuis un fichier XML de la version 2. - * - * @param inputUI inputUI - */ - public void importV2Region(InputUI inputUI) { - - setStatusMessage(inputUI, t("isisfish.message.import.xml.v2.file"), true); - - try { - File file = FileUtil.getFile(".*.xml$", t("isisfish.message.import.region.xml")); - if (file != null) { - new ImportFromV2(true).importXML(file); - - refreshRegionList(inputUI, null); - } - } catch (Exception eee) { - throw new IsisFishRuntimeException(t("isisfish.error.region.import"), eee); - } - - setStatusMessage(inputUI, t("isisfish.message.import.finished")); - } - - /** * Extract from a simulation the region, and rename it with name given * by user. * Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/input/InputUI.jaxx =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/input/InputUI.jaxx 2014-06-16 16:04:46 UTC (rev 4017) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/input/InputUI.jaxx 2014-06-17 09:02:25 UTC (rev 4018) @@ -32,7 +32,6 @@ <JMenu text="isisfish.common.region"> <JMenuItem text="isisfish.input.menu.importRegion" onActionPerformed="getHandler().importRegion(this)" /> <JMenuItem text="isisfish.input.menu.importRenameRegion" onActionPerformed="getHandler().importRegionAndRename(this)" /> - <JMenuItem text="isisfish.input.menu.importRegionV2" onActionPerformed="getHandler().importV2Region(this)" /> <JMenuItem text="isisfish.input.menu.importRegionSimulation" onActionPerformed="getHandler().importRegionFromSimulation(this)" /> <JMenuItem text="isisfish.input.menu.exportRegion" enabled='{isRegionLoaded()}' onActionPerformed="getHandler().exportRegion(this)" /> <JMenuItem text="isisfish.input.menu.copyRegion" enabled='{isRegionLoaded()}' onActionPerformed="getHandler().copyRegion(this)" /> Modified: trunk/src/main/resources/i18n/isis-fish_en_GB.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2014-06-16 16:04:46 UTC (rev 4017) +++ trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2014-06-17 09:02:25 UTC (rev 4018) @@ -211,6 +211,7 @@ isisfish.config.main.simulation.ssh.pbsbinpath.description=PBS executables (qsub, qdel...) directory isisfish.config.main.simulation.ssh.pbsqsuboptions=Qsub arguments isisfish.config.main.simulation.ssh.pbsqsuboptions.description=Arguments used at qsub job sumbit. Default to '-m n' don't send mail. +isisfish.config.main.simulation.ssh.proxy.command.description= isisfish.config.main.simulation.ssh.server=Simulation server isisfish.config.main.simulation.ssh.server.description=Simulation server address isisfish.config.main.simulation.ssh.tmppath=Server temp directory Modified: trunk/src/main/resources/i18n/isis-fish_fr_FR.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2014-06-16 16:04:46 UTC (rev 4017) +++ trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2014-06-17 09:02:25 UTC (rev 4018) @@ -211,6 +211,7 @@ isisfish.config.main.simulation.ssh.pbsbinpath.description=Emplacement des commandes PBS (qsub, qdel...) sur le serveur isisfish.config.main.simulation.ssh.pbsqsuboptions=Arguments qsub isisfish.config.main.simulation.ssh.pbsqsuboptions.description=Arguments utilisés lors de la soumission des jobs. Par défaut '-m n' pas d'envoi de mails. +isisfish.config.main.simulation.ssh.proxy.command.description= isisfish.config.main.simulation.ssh.server=Serveur de simulation isisfish.config.main.simulation.ssh.server.description=Adresse du serveur de simulation isisfish.config.main.simulation.ssh.tmppath=Dossier temporaire

1 0

r4017 - trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher
by echatellier＠users.forge.codelutin.com June 16, 2014

June 16, 2014

Author: echatellier Date: 2014-06-16 18:04:46 +0200 (Mon, 16 Jun 2014) New Revision: 4017 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4017 Log: fixes #5244: Les plans de simulations continuent alors que la simulation n'a pas encore ?\195?\169t?\195?\169 t?\195?\169l?\195?\169charg?\195?\169es depuis caparmor Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java 2014-06-16 15:21:40 UTC (rev 4016) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java 2014-06-16 16:04:46 UTC (rev 4017) @@ -356,8 +356,7 @@ // make sure user is connected try { getSSHSession(); - } - catch(JSchException e) { + } catch(JSchException e) { throw new RemoteException("Can't connect", e); } @@ -399,7 +398,6 @@ // MD5 + SIMULATION zip file // FIXME echatellier 20140402 check not yet existing md5ControlFile and simulation ended - // simulation result will never be downloaded try { File md5ControlFile = downloadResultsMD5File(sshSession, control.getId()); @@ -434,8 +432,7 @@ // control need to be read before, otherwize, setText // in clearSimulationFiles will erase file :( clearSimulationFiles(sshSession, control); - } - else { + } else { if (log.isWarnEnabled()) { log.warn("Simulation zip download failed"); } @@ -444,8 +441,7 @@ // remove temp file md5ControlFile.delete(); } - } - catch(SSHException e) { + } catch(SSHException e) { if (log.isDebugEnabled()) { log.debug(t("Can't download archive : %s", e.getMessage())); } Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java 2014-06-16 15:21:40 UTC (rev 4016) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java 2014-06-16 16:04:46 UTC (rev 4017) @@ -527,8 +527,7 @@ if (control.isStopSimulationRequest()) { launcher.simulationStopRequest(job); simulationEnded = true; - } - else { + } else { launcher.updateControl(service, control); // by default, Progress = ProgressMax = 0 @@ -536,18 +535,20 @@ // and set by end of // fr.ifremer.isisfish.simulator.launcher.InProcessSimulatorLauncher#localSimulateSameThread(SimulationControl, SimulationStorage) - File simulationRoot = SimulationStorage.getSimulationDirectory(control.getId()); + File localControlFile = SimulationStorage.getSimulationControlFile(control.getId()); // si la simulation n'est pas localement presente, c'est pas fini - if (simulationRoot.isDirectory()) { + // la simulation peut être finie, mais non téléchargées + // en testant le fichier de controle, on s'assure que la simulation est physiquement + // présente en local + if (localControlFile.isFile()) { // cas d'une simulation terminée if (control.getProgress() > 0 && control.getProgress() >= control.getProgressMax()) { simulationEnded = true; - } - else { - + } else { // cas d'une simulation arretee par exception + File simulationRoot = SimulationStorage.getSimulationDirectory(control.getId()); File informationFile = SimulationStorage.getSimulationInformationFile(simulationRoot); SimulationInformation information = new SimulationInformation(informationFile); if (StringUtils.isNotEmpty(information.getException())) {

1 0

r4016 - in trunk/src/main/java/fr/ifremer/isisfish: . simulator/launcher ui/config util/ssh
by echatellier＠users.forge.codelutin.com June 16, 2014

June 16, 2014

Author: echatellier Date: 2014-06-16 17:21:40 +0200 (Mon, 16 Jun 2014) New Revision: 4016 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4016 Log: Support jsch proxy command to allow using caparmor outside ifremer network Added: trunk/src/main/java/fr/ifremer/isisfish/util/ssh/ProxyCommand.java Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigAction.java Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-06-16 11:46:42 UTC (rev 4015) +++ trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-06-16 15:21:40 UTC (rev 4016) @@ -181,7 +181,9 @@ public IsisConfig() { for (Option o : Option.values()) { - setDefaultOption(o.key, o.defaultValue); + if (o.defaultValue != null) { + setDefaultOption(o.key, o.defaultValue); + } } for (Action a : Action.values()) { @@ -666,11 +668,15 @@ setOption(Option.SSH_KEY_FILE.key, sshFile.getAbsolutePath()); } - /*public boolean isUseVCS() { - String value = getOption(Option.VCS_TYPE.key); - boolean result = !VCSNone.TYPE_NONE.equals(value); + /** + * La proxy command a ajouter pour pouvoir contacter le serveur cible. + * + * @return ssh proxy command + */ + public String getSimulatorSshProxyCommand() { + String result = getOption(Option.SIMULATOR_SSH_PROXYCOMMAND.key); return result; - }*/ + } /** * Get launch.ui option value. @@ -1014,6 +1020,8 @@ SIMULATOR_SSH_MAXTHREADS("simulation.ssh.max.threads", n("isisfish.config.main.simulation.ssh.max.threads.description"), "1"), /** Serveur accessible par SSH : mémoire (Xmx) allouée pour les process java sur caparmor */ SIMULATOR_SSH_MAXMEMORY("simulation.ssh.max.memory", n("isisfish.config.main.simulation.ssh.max.memory.description"), "2000M"), + /** Serveur accessible par SSH : la proxy commande a ajouter pour ouvrir la connexion. */ + SIMULATOR_SSH_PROXYCOMMAND("simulation.ssh.proxy.command", n("isisfish.config.main.simulation.ssh.proxy.command.description"), null), /** Application locale (for i18n init). */ LOCALE("locale", n("isisfish.config.main.locale.description"), "fr_FR"), Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java 2014-06-16 11:46:42 UTC (rev 4015) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java 2014-06-16 15:21:40 UTC (rev 4016) @@ -57,6 +57,7 @@ import fr.ifremer.isisfish.simulator.SimulationControl; import fr.ifremer.isisfish.util.ssh.InvalidPassphraseException; import fr.ifremer.isisfish.util.ssh.ProgressMonitor; +import fr.ifremer.isisfish.util.ssh.ProxyCommand; import fr.ifremer.isisfish.util.ssh.SSHAgent; import fr.ifremer.isisfish.util.ssh.SSHException; import fr.ifremer.isisfish.util.ssh.SSHUserInfo; @@ -301,7 +302,7 @@ sshSession, control.getId(), simulationPrescript); // start simulation if necessary (multi jobs) ... - startSimulation(simulationItem, simulationid, simulationRemotePath, remoteResultZip, simulationPreScriptPath); + startSimulation(sshSession, simulationItem, simulationid, simulationRemotePath, remoteResultZip, simulationPreScriptPath); } catch (Exception e) { if (log.isErrorEnabled()) { @@ -565,6 +566,12 @@ Session session = jsch.getSession(username, host, port); + // add proxy command if specified + String proxyCommand = IsisFish.config.getSimulatorSshProxyCommand(); + if (StringUtils.isNotBlank(proxyCommand)) { + session.setProxy(new ProxyCommand(proxyCommand)); + } + // username and password will be given via UserInfo interface. SSHUserInfo ui = new SSHUserInfo(); if (sshKeyUsed) { @@ -987,6 +994,7 @@ * * Current simulation can be started later with a PBS multi job. * + * @param session ssh session * @param simulationItem simulation item (needed for additionnal info, simulation, number, indenpendant, etc...) * @param simulationid simulation id * @param simulationRemoteZipPath simulation preparation (input) zip path @@ -995,7 +1003,7 @@ * * @throws Exception */ - protected void startSimulation(SimulationItem simulationItem, String simulationid, String simulationRemoteZipPath, String remoteResultZip, String simulationPreScriptPath) throws Exception { + protected void startSimulation(Session session, SimulationItem simulationItem, String simulationid, String simulationRemoteZipPath, String remoteResultZip, String simulationPreScriptPath) throws Exception { // standalone simulation // no question, generate script, launch it each time @@ -1003,12 +1011,12 @@ // single simulation File simulationPSBScript = getLaunchSimulationScriptFile(simulationid, simulationRemoteZipPath, true, remoteResultZip, simulationPreScriptPath, false); - String scriptRemotePath = uploadSimulationScript(sshSession, simulationid, simulationPSBScript); + String scriptRemotePath = uploadSimulationScript(session, simulationid, simulationPSBScript); // prescript uploaded, delete simulationPSBScript.delete(); - sendStartSimulationRequest(sshSession, simulationid, scriptRemotePath, -1); + sendStartSimulationRequest(session, simulationid, scriptRemotePath, -1); } else { // standalone, on do it for last simulation @@ -1022,13 +1030,13 @@ // multiples jobs simulation File simulationPSBScript = getLaunchSimulationScriptFile(shortSimulationId, simulationRemoteZipPath, simulationItem.isStandaloneSimulationZip(), remoteResultZip, simulationPreScriptPath, true); - String scriptRemotePath = uploadSimulationScript(sshSession, shortSimulationId, simulationPSBScript); + String scriptRemotePath = uploadSimulationScript(session, shortSimulationId, simulationPSBScript); // prescript uploaded, delete simulationPSBScript.delete(); // file will be named with shortSimulationId (instead of simulationId) - sendStartSimulationRequest(sshSession, shortSimulationId, scriptRemotePath, simulationItem.getSimulationNumber()); + sendStartSimulationRequest(session, shortSimulationId, scriptRemotePath, simulationItem.getSimulationNumber()); } else { if (log.isDebugEnabled()) { Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigAction.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigAction.java 2014-06-16 11:46:42 UTC (rev 4015) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigAction.java 2014-06-16 15:21:40 UTC (rev 4016) @@ -47,6 +47,7 @@ import fr.ifremer.isisfish.IsisFish; import fr.ifremer.isisfish.util.ssh.InvalidPassphraseException; +import fr.ifremer.isisfish.util.ssh.ProxyCommand; import fr.ifremer.isisfish.util.ssh.SSHAgent; import fr.ifremer.isisfish.util.ssh.SSHException; import fr.ifremer.isisfish.util.ssh.SSHUserInfo; @@ -287,6 +288,10 @@ } Session session = jsch.getSession(currentSSHUsername, host, port); + String proxyCommand = IsisFish.config.getSimulatorSshProxyCommand(); + if (StringUtils.isNotBlank(proxyCommand)) { + session.setProxy(new ProxyCommand(proxyCommand)); + } // username and password will be given via UserInfo interface. SSHUserInfo ui = new SSHUserInfo(); @@ -441,7 +446,11 @@ } Session session = jsch.getSession(currentSSHUsername, host, port); - + String proxyCommand = IsisFish.config.getSimulatorSshProxyCommand(); + if (StringUtils.isNotBlank(proxyCommand)) { + session.setProxy(new ProxyCommand(proxyCommand)); + } + // username and password will be given via UserInfo interface. SSHUserInfo ui = new SSHUserInfo(); if (sshKeyUsed) { Added: trunk/src/main/java/fr/ifremer/isisfish/util/ssh/ProxyCommand.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/ssh/ProxyCommand.java (rev 0) +++ trunk/src/main/java/fr/ifremer/isisfish/util/ssh/ProxyCommand.java 2014-06-16 15:21:40 UTC (rev 4016) @@ -0,0 +1,84 @@ +/* + * #%L + * IsisFish + * + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2014 Ifremer, Code Lutin, Chatellier Eric + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ + +package fr.ifremer.isisfish.util.ssh; + +import java.io.IOException; +import java.io.InputStream; +import java.io.OutputStream; +import java.net.Socket; + +import com.jcraft.jsch.Proxy; +import com.jcraft.jsch.SocketFactory; + +/** + * Implementation du proxy commande pour pouvoir utiliser un proxy local dans le + * but de faire un rebond à travers un serveur intermédiaire. + * + * @author Eric Chatellier + */ +public class ProxyCommand implements Proxy { + protected String command; + protected Process p = null; + protected InputStream in = null; + protected OutputStream out = null; + + public ProxyCommand(String command) { + this.command = command; + } + + public void connect(SocketFactory socket_factory, String host, int port, int timeout) throws Exception { + String fullCommand = command.replace("%h", host); + fullCommand = fullCommand.replace("%p", new Integer(port).toString()); + p = Runtime.getRuntime().exec(fullCommand); + in = p.getInputStream(); + out = p.getOutputStream(); + } + + public Socket getSocket() { + return null; + } + + public InputStream getInputStream() { + return in; + } + + public OutputStream getOutputStream() { + return out; + } + + public void close() { + try { + if (p != null) { + p.getErrorStream().close(); + p.getOutputStream().close(); + p.getInputStream().close(); + p.destroy(); + p = null; + } + } catch (IOException e) { + } + } +} Property changes on: trunk/src/main/java/fr/ifremer/isisfish/util/ssh/ProxyCommand.java ___________________________________________________________________ Added: svn:eol-style + native Added: svn:keywords + Author Date Id Revision HeadURL

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r4015 - in trunk: . src/main/java/fr/ifremer/isisfish
by echatellier＠users.forge.codelutin.com June 16, 2014

June 16, 2014

Author: echatellier Date: 2014-06-16 13:46:42 +0200 (Mon, 16 Jun 2014) New Revision: 4015 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4015 Log: Update libs Modified: trunk/pom.xml trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-06-12 10:49:10 UTC (rev 4014) +++ trunk/pom.xml 2014-06-16 11:46:42 UTC (rev 4015) @@ -20,7 +20,7 @@ <dependency> <groupId>org.nuiton</groupId> <artifactId>nuiton-utils</artifactId> - <version>3.0-rc-2</version> + <version>3.0-rc-3</version> <scope>compile</scope> </dependency> @@ -111,15 +111,14 @@ <artifactId>mail</artifactId> <version>1.4.7</version> <scope>compile</scope> + <exclusions> + <exclusion> + <artifactId>activation</artifactId> + <groupId>javax.activation</groupId> + </exclusion> + </exclusions> </dependency> - <dependency> - <groupId>javax.activation</groupId> - <artifactId>activation</artifactId> - <version>1.1.1</version> - <scope>compile</scope> - </dependency> -  <dependency> <groupId>org.nuiton.jaxx</groupId> @@ -198,6 +197,12 @@ <groupId>org.apache.commons</groupId> <artifactId>commons-email</artifactId> <version>1.3.2</version> + <exclusions> + <exclusion> + <artifactId>activation</artifactId> + <groupId>javax.activation</groupId> + </exclusion> + </exclusions> </dependency> <dependency> @@ -469,7 +474,7 @@ <signatureVersion>1.0</signatureVersion>  - <jaxxVersion>2.8.5</jaxxVersion> + <jaxxVersion>2.8.7</jaxxVersion> <eugeneVersion>2.7.4</eugeneVersion> <topiaVersion>2.9-rc-1</topiaVersion> <hibernateVersion>4.3.5.Final</hibernateVersion> Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-06-12 10:49:10 UTC (rev 4014) +++ trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-06-16 11:46:42 UTC (rev 4015) @@ -120,7 +120,7 @@ * migration de donnees demande automatiquement un changement de version * d'application. */ - protected final static Version version = new Version(4, 3, 0, 1); + protected final static Version version = new Version(4, 3, 0, 2); protected final static Version majorVersion = new Version(version.getNumber(0)); protected final static Version databaseVersion = new Version(

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r4014 - trunk/src/main/java/fr/ifremer/isisfish/simulator
by echatellier＠users.forge.codelutin.com June 12, 2014

June 12, 2014

Author: echatellier Date: 2014-06-12 12:49:10 +0200 (Thu, 12 Jun 2014) New Revision: 4014 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4014 Log: Escape (again) factor name for equations Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-06-10 17:15:10 UTC (rev 4013) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-06-12 10:49:10 UTC (rev 4014) @@ -376,7 +376,13 @@ * @param value value */ public void setComputeValue(String key, Double value) { - contextEquationValue.put(key, value); + + // on echappe (encore) le nom du facteur, car pour une raison ou pour une autre, + // l'echapement de la méthode fr.ifremer.isisfish.simulator.launcher.SimulationService.fillDesignPlanNominalValue(TopiaContext, DesignPlan) + // n'a pas l'air de suffir pour les equations :( + + String localKey = SensitivityUtils.espaceFactorName(key); + contextEquationValue.put(localKey, value); } /**

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[ANN] - IsisFish 4.3.0.1 released
by codelutin.com Release Notification June 10, 2014

June 10, 2014

The IsisFish team is pleased to announce the isis-fish-4.3.0.1 release! Simulateur de pecherie complexe. Documentation of the project can be found here: http://doc.codelutin.com/isis-fish Changes ------- Changes in this version include: Fixed Bugs: o Update to nuiton-matrix- 2.4.1 Issue: 5198. Thanks to Eric Chatellier. Resolved by echatellier. o Can't run sensitivity analysis since 4.3.0.0 Issue: 5197. Thanks to Eric Chatellier. Resolved by echatellier. Downloads --------- For a manual installation, you can download files here: http://forge.codelutin.com/projects/isis-fish/files * isis-fish-4.3.0.1-bin.zip - http://forge.codelutin.com/attachments/download/1914 Maven artifacts --------------- Artifacts are deployed in nuiton maven repository http://maven.nuiton.org/other-releases/ Have fun! -IsisFish team

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r4013 - trunk
by echatellier＠users.forge.codelutin.com June 10, 2014

June 10, 2014

Author: echatellier Date: 2014-06-10 19:15:10 +0200 (Tue, 10 Jun 2014) New Revision: 4013 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4013 Log: [maven-release-plugin] prepare for next development iteration Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-06-10 17:15:05 UTC (rev 4012) +++ trunk/pom.xml 2014-06-10 17:15:10 UTC (rev 4013) @@ -11,7 +11,7 @@ <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.3.0.1</version> + <version>4.3.0.2-SNAPSHOT</version>  <dependencies> @@ -667,9 +667,9 @@   <scm> - <connection>scm:svn:https://svn.codelutin.com/isis-fish/tags/isis-fish-4.3.0.1</connection> - <developerConnection>scm:svn:https://svn.codelutin.com/isis-fish/tags/isis-fish-4.3.0.1</developerConnection> - <url>https://svn.codelutin.com/isis-fish/tags/isis-fish-4.3.0.1</url> + <connection>scm:svn:https://svn.codelutin.com/isis-fish/trunk</connection> + <developerConnection>scm:svn:https://svn.codelutin.com/isis-fish/trunk</developerConnection> + <url>https://svn.codelutin.com/isis-fish/trunk</url> </scm> <repositories>

1 0

r4012 - in tags: . isis-fish-4.3.0.1
by echatellier＠users.forge.codelutin.com June 10, 2014

June 10, 2014

Author: echatellier Date: 2014-06-10 19:15:05 +0200 (Tue, 10 Jun 2014) New Revision: 4012 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4012 Log: [maven-release-plugin] copy for tag isis-fish-4.3.0.1 Added: tags/isis-fish-4.3.0.1/ Property changes on: tags/isis-fish-4.3.0.1 ___________________________________________________________________ Added: svn:mergeinfo + /branches/4.0.0-svnkit:3665-3698 /branches/4.0.1:3616-3968 /branches/4.1:3601-3670 Added: svn:ignore + maven.log target velocity.log .classpath .project isis-fish.ipr isis-fish.iws isis-fish.iml .settings bin nbproject Inputs_Langoustine .idea

1 0

r4011 - trunk
by echatellier＠users.forge.codelutin.com June 10, 2014

June 10, 2014

Author: echatellier Date: 2014-06-10 19:14:56 +0200 (Tue, 10 Jun 2014) New Revision: 4011 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4011 Log: [maven-release-plugin] prepare release isis-fish-4.3.0.1 Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-06-10 17:08:58 UTC (rev 4010) +++ trunk/pom.xml 2014-06-10 17:14:56 UTC (rev 4011) @@ -11,7 +11,7 @@ <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.3.0.1-SNAPSHOT</version> + <version>4.3.0.1</version>  <dependencies> @@ -667,9 +667,9 @@   <scm> - <connection>scm:svn:https://svn.codelutin.com/isis-fish/trunk</connection> - <developerConnection>scm:svn:https://svn.codelutin.com/isis-fish/trunk</developerConnection> - <url>https://svn.codelutin.com/isis-fish/trunk</url> + <connection>scm:svn:https://svn.codelutin.com/isis-fish/tags/isis-fish-4.3.0.1</connection> + <developerConnection>scm:svn:https://svn.codelutin.com/isis-fish/tags/isis-fish-4.3.0.1</developerConnection> + <url>https://svn.codelutin.com/isis-fish/tags/isis-fish-4.3.0.1</url> </scm> <repositories>

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