Author: echatellier Date: 2012-05-14 11:53:20 +0200 (Mon, 14 May 2012) New Revision: 3699 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3699 Log: Merge trunk and branches/4.0.0-svnkit Modified: branches/4.0.1/ branches/4.0.1/pom.xml branches/4.0.1/src/license/THIRD-PARTY.properties branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisConfig.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/migration/MigrationV40V41.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationServiceTableModel.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/simulator/ParamsUI.jaxx branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/simulator/RuleChooser.jaxx branches/4.0.1/src/main/resources/templates/ssh/qsub-script.ftl branches/4.0.1/src/main/xmi/isis-fish.properties branches/4.0.1/src/site/rst/documentation/devel/rcaparmor.rst branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/launcher/SshSimulatorLauncherTest.java Property changes on: branches/4.0.1 ___________________________________________________________________ Modified: svn:mergeinfo - /branches/4.1:3601-3670 /trunk:3616-3672 + /branches/4.0.0-svnkit:3665-3698 /branches/4.1:3601-3670 /trunk:3616-3698 Modified: branches/4.0.1/pom.xml =================================================================== --- branches/4.0.1/pom.xml 2012-05-11 12:05:56 UTC (rev 3698) +++ branches/4.0.1/pom.xml 2012-05-14 09:53:20 UTC (rev 3699) @@ -89,7 +89,7 @@ <dependency> <groupId>com.fifesoft</groupId> <artifactId>rsyntaxtextarea</artifactId> - <version>1.5.0</version> + <version>2.0.2</version> <scope>runtime</scope> </dependency> @@ -173,7 +173,7 @@ <dependency> <groupId>commons-io</groupId> <artifactId>commons-io</artifactId> - <version>2.2</version> + <version>2.3</version> </dependency> <dependency> @@ -259,7 +259,7 @@ <dependency> <groupId>com.jcraft</groupId> <artifactId>jsch</artifactId> - <version>0.1.46</version> + <version>0.1.48</version> <scope>compile</scope> </dependency> @@ -292,7 +292,7 @@ <dependency> <groupId>com.h2database</groupId> <artifactId>h2</artifactId> - <version>1.3.165</version> + <version>1.3.166</version> <scope>compile</scope> </dependency> @@ -379,7 +379,7 @@ <dependency> <groupId>org.tmatesoft.svnkit</groupId> <artifactId>svnkit</artifactId> - <version>1.3.5</version> + <version>1.7.4-v1</version> <scope>compile</scope> </dependency> <!-- fin svnkit pour communication subversion --> @@ -540,7 +540,7 @@ <eugeneVersion>2.4.2</eugeneVersion> <topiaVersion>2.6.9</topiaVersion> <hibernateVersion>3.6.10.Final</hibernateVersion> - <nuitonUtilsVersion>2.4.6</nuitonUtilsVersion> + <nuitonUtilsVersion>2.4.7</nuitonUtilsVersion> <nuitonI18nVersion>2.4.1</nuitonI18nVersion> <nuitonWidgetsVersion>1.1.1</nuitonWidgetsVersion> <aspectwerkzVersion>2.0</aspectwerkzVersion> Modified: branches/4.0.1/src/license/THIRD-PARTY.properties =================================================================== --- branches/4.0.1/src/license/THIRD-PARTY.properties 2012-05-11 12:05:56 UTC (rev 3698) +++ branches/4.0.1/src/license/THIRD-PARTY.properties 2012-05-14 09:53:20 UTC (rev 3699) @@ -7,11 +7,11 @@ # - Apache Software License Version 2.0 # - Apache Software License, Version 1.1 # - Apache Software License, Version 2.0 -# - BBN Technologies # - BSD License # - BSD licence # - BSD style # - BSD-style license +# - Bouncy Castle License # - CDDL # - COMMON DEVELOPMENT AND DISTRIBUTION LICENSE (CDDL) Version 1.0 # - Common Public License Version 1.0 @@ -30,11 +30,13 @@ # - Lesser General Public License (LPGL) # - Lesser General Public License (LPGL) v 2.1 # - MIT License +# - MPL 1.1 +# - Mozilla Public License +# - OpenMap Software License Agreement # - Revised BSD # - Sun's Binary Code License # - The Apache Software License, Version 2.0 # - The H2 License, Version 1.0 -# - http://asm.ow2.org/license.html # - http://sqljet.com/ # - http://svnkit.com/license.html # - http://www.trilead.com/Products/Trilead_SSH_for_Java/License/ @@ -43,10 +45,8 @@ # Please fill the missing licenses for dependencies : # # -#Fri Nov 18 15:56:18 CET 2011 +#Thu Apr 26 16:37:35 CEST 2012 antlr--antlr--2.7.6=BSD License -asm--asm-commons--3.1=http\://asm.ow2.org/license.html -asm--asm-tree--3.1=http\://asm.ow2.org/license.html aspectwerkz--aspectwerkz--2.0=GNU Lesser General Public License aspectwerkz--aspectwerkz-core--2.0=GNU Lesser General Public License aspectwerkz--aspectwerkz-jdk5--2.0=GNU Lesser General Public License @@ -55,7 +55,6 @@ commons-jxpath--commons-jxpath--1.3=The Apache Software License, Version 2.0 commons-primitives--commons-primitives--1.0=The Apache Software License, Version 2.0 dom4j--dom4j--1.6.1=BSD License -javassist--javassist--3.8.0.GA=GNU Lesser General Public License javax.activation--activation--1.1.1=COMMON DEVELOPMENT AND DISTRIBUTION LICENSE (CDDL) Version 1.0 javax.transaction--jta--1.1=Java Transaction API (JTA) License jaxen--jaxen--1.1.1=Jaxen license Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2012-05-11 12:05:56 UTC (rev 3698) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2012-05-14 09:53:20 UTC (rev 3699) @@ -912,7 +912,7 @@ SIMULATOR_LAUNCHER_REMOTE(SimulationService.SIMULATION_LAUNCHER + ".2", n_("isisfish.config.main.remoteCaparmor.description"), SSHSimulatorLauncher.class.getName()), /** Serveur accessible par ssh : address */ - SIMULATOR_SSH_SERVER("simulation.ssh.server", n_("isisfish.config.main.simulation.ssh.server.description"), "caparmor"), + SIMULATOR_SSH_SERVER("simulation.ssh.server", n_("isisfish.config.main.simulation.ssh.server.description"), "caparmor-sftp"), /** Serveur accessible par ssh : login */ SIMULATOR_SSH_USER_NAME("simulation.ssh.username", n_("isisfish.config.main.simulation.ssh.username.description"), ""), /** Serveur accessible par ssh : user home directory */ Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java 2012-05-11 12:05:56 UTC (rev 3698) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java 2012-05-14 09:53:20 UTC (rev 3699) @@ -116,6 +116,17 @@ } } + /** + * Result can be removed from cache when computed result (from multiple step) + * become invalidated by new step result. + * + * @param name result name to remove + */ + protected void removeInCache(String name) { + cache.remove(name); + cacheContext.remove(name); + } + protected MatrixND getInCache(TimeStep step, String name) { // do not use toString for step (depend on i18n) String key = step.getStep() + ":" + name; @@ -357,6 +368,12 @@ addAvailableResult(step, name); putInCache(step, name, newMat, tx); + + // remove from cache result computed by #getMatrix(name) + // beacause, if a new step is added, result become false + // but DO NOT REMOVE result named step + name + removeInCache(name); + } catch (TopiaException eee) { log.warn("Can't add result '" + name + "' at step " + step, eee); } @@ -518,8 +535,20 @@ /** * Retourne une matrice contenant tous les pas de temps. + * @param pop la population pour lequel on souhaite la matrice * @param name le nom des resultats dont on veut une matrice globale. + * @param tx la transaction a utiliser + * @since 4.1.0.0 */ + public MatrixND getMatrix(Population pop, String name, TopiaContext tx) { + String newName = name + " " + pop; + return getMatrix(newName, tx); + } + + /** + * Retourne une matrice contenant tous les pas de temps. + * @param name le nom des resultats dont on veut une matrice globale. + */ public MatrixND getMatrix(String name) { MatrixND resultMat = null; try { Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/migration/MigrationV40V41.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/migration/MigrationV40V41.java 2012-05-11 12:05:56 UTC (rev 3698) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/migration/MigrationV40V41.java 2012-05-14 09:53:20 UTC (rev 3699) @@ -34,7 +34,7 @@ import org.nuiton.util.Version; /** - * Migration between version 3.3 and 4.0. + * Migration between version 4.0 and 4.1. * * @author chatellier * @version $Revision$ @@ -77,6 +77,5 @@ "MATRIXVALUE_SEMANTICS LONGVARCHAR," + "MATRIXVALUE_DATA LONGVARCHAR, " + "EQUATIONVALUE VARCHAR(255)) "); - } } Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationServiceTableModel.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationServiceTableModel.java 2012-05-11 12:05:56 UTC (rev 3698) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationServiceTableModel.java 2012-05-14 09:53:20 UTC (rev 3699) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2002 - 2010 Ifremer, Code Lutin, Benjamin Poussin + * Copyright (C) 2002 - 2012 Ifremer, Code Lutin, Benjamin Poussin, 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 @@ -97,11 +97,11 @@ boolean forDoToJobs) { this.simulationService = simulationService; if (forDoToJobs) { - jobListener = new JobToDoListener(simulationService, this); + jobListener = new JobToDoListener(this); } else { - jobListener = new JobDoneListener(simulationService, this); + jobListener = new JobDoneListener(this); } - controlListener = new ControlListener(simulationService, this); + controlListener = new ControlListener(this); simulationService.addSimulationServiceListener(jobListener); jobListener.setData(); } @@ -209,19 +209,23 @@ */ public Object getValueAt(int rowIndex, int columnIndex) { - // TODO IndexOutOfBoundException here - // Concurrent problem ? + // FIXME echatellier : hack ArrayIndexOutOfBoundException for unknown + // reason (very hard to fix properly) if (rowIndex >= jobs.size()) { - return null; + if (columnIndex == 4) { + return new JProgressBar(); // NPE + } else { + return null; + } } + Object result = ""; + SimulationJob job = jobs.get(rowIndex); SimulationControl control = job.getItem().getControl(); String id = control.getId(); SimulationParameter param = job.getItem().getParameter(); - Object result = ""; - if (log.isTraceEnabled()) { log.trace("Update table model : " + "id = " + control.getId() + ", " + "control.getProgress() = " + control.getProgress() @@ -286,12 +290,9 @@ class JobDoneListener implements AbstractJobListener, SimulationServiceListener { - protected SimulationService simulationService; protected SimulationServiceTableModel model; - public JobDoneListener(SimulationService simulationService, - SimulationServiceTableModel model) { - this.simulationService = simulationService; + public JobDoneListener(SimulationServiceTableModel model) { this.model = model; setData(); } @@ -321,12 +322,9 @@ class JobToDoListener implements AbstractJobListener, SimulationServiceListener { - protected SimulationService simulationService; protected SimulationServiceTableModel model; - public JobToDoListener(SimulationService simulationService, - SimulationServiceTableModel model) { - this.simulationService = simulationService; + public JobToDoListener(SimulationServiceTableModel model) { this.model = model; setData(); } @@ -362,12 +360,9 @@ protected class ControlListener implements PropertyChangeListener { - protected SimulationService simulationService; protected SimulationServiceTableModel model; - public ControlListener(SimulationService simulationService, - SimulationServiceTableModel model) { - this.simulationService = simulationService; + public ControlListener(SimulationServiceTableModel model) { this.model = model; } Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/simulator/ParamsUI.jaxx =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/simulator/ParamsUI.jaxx 2012-05-11 12:05:56 UTC (rev 3698) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/simulator/ParamsUI.jaxx 2012-05-14 09:53:20 UTC (rev 3699) @@ -195,10 +195,10 @@ setExportSens(); setSensitivityAnalysis(); setFactor(); - + // regles ruleChooser.setRulesList(simulAction.getSimulationParameter().getRules()); - + getParentContainer(WelcomePanelUI.class).setStatusMessage(_("isisfish.message.old.simulation.loaded")); } }); Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/simulator/RuleChooser.jaxx =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/simulator/RuleChooser.jaxx 2012-05-11 12:05:56 UTC (rev 3698) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/simulator/RuleChooser.jaxx 2012-05-14 09:53:20 UTC (rev 3699) @@ -51,11 +51,10 @@ addPropertyChangeListener(PROPERTY_RULES_LIST, new PropertyChangeListener() { public void propertyChange(PropertyChangeEvent evt) { if (evt.getNewValue() == null) { - selectedRulesList.setModel(new RuleListModel()); - } - else /*if (evt.getNewValue() != null)*/ { + selectedRulesListModel.setRules(new ArrayList<Rule>()); + } else { List<Rule> rules = (List<Rule>)evt.getNewValue(); - selectedRulesList.setModel(new RuleListModel(rules)); + selectedRulesListModel.setRules(rules); } } }); Modified: branches/4.0.1/src/main/resources/templates/ssh/qsub-script.ftl =================================================================== --- branches/4.0.1/src/main/resources/templates/ssh/qsub-script.ftl 2012-05-11 12:05:56 UTC (rev 3698) +++ branches/4.0.1/src/main/resources/templates/ssh/qsub-script.ftl 2012-05-14 09:53:20 UTC (rev 3699) @@ -26,8 +26,7 @@ cd "${isishome}" -setenv R_HOME /home3/caparmor/poussin/R/lib64/R -setenv PATH ${r"${R_HOME}"}/bin:${r"${PATH}"} +setenv R_HOME /appli/R/2.15.0-gnu-4.3/lib64/R setenv LD_LIBRARY_PATH ${r"${R_HOME}"}/lib <#assign commonCommand="${javapath} -Djava.library.path=jri64 -DR.type=jni -Xmx2000M -jar isis-fish*.jar" /> Modified: branches/4.0.1/src/main/xmi/isis-fish.properties =================================================================== --- branches/4.0.1/src/main/xmi/isis-fish.properties 2012-05-11 12:05:56 UTC (rev 3698) +++ branches/4.0.1/src/main/xmi/isis-fish.properties 2012-05-14 09:53:20 UTC (rev 3699) @@ -57,3 +57,6 @@ fr.ifremer.isisfish.entities.Variable.attribute.entityId.tagvalue.notNull=true fr.ifremer.isisfish.entities.VesselType.class.tagvalue.contextable=true fr.ifremer.isisfish.entities.Zone.class.tagvalue.contextable=true + +#�fix lazy exception on sensitivity export +fr.ifremer.isisfish.entities.Population.attribute.maturityOgiveEquation.tagvalue.lazy=false Modified: branches/4.0.1/src/site/rst/documentation/devel/rcaparmor.rst =================================================================== --- branches/4.0.1/src/site/rst/documentation/devel/rcaparmor.rst 2012-05-11 12:05:56 UTC (rev 3698) +++ branches/4.0.1/src/site/rst/documentation/devel/rcaparmor.rst 2012-05-14 09:53:20 UTC (rev 3699) @@ -1,3 +1,27 @@ +.. - +.. * #%L +.. * IsisFish +.. * +.. * $Id$ +.. * $HeadURL$ +.. * %% +.. * Copyright (C) 2012 CodeLutin, 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 2 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-2.0.html>. +.. * #L% +.. - Utilisation de R sur caparmor ============================= @@ -4,16 +28,14 @@ Version caparmor ---------------- -La version de R fournie par caparmor n'est pas utilisable:: +La version de R doit avoir été compilée avec l'option par "--enable-R-shlib" +sinon, le fichier "libR.so" est manquant:: ll /appli/R/2.14.2-gnu-4.3/lib64/R/lib -rwxr-xr-x 1 root root 467061 Mar 5 14:13 libRblas.so -rwxr-xr-x 1 root root 3977966 Mar 5 14:13 libRlapack.so -Il manque le fichier "libR.so" parce que R n'a pas été compilé avec l'option -"--enable-R-shlib". - Recompilation de R ------------------ @@ -34,7 +56,7 @@ Installation des librairies pour la version que l'on vient de compiler:: - /home3/caparmor/poussin/R-2.15/bin/R + module load R/2.15.0-gnu-4.3 install.packages("FLCore", repos="http://flr-project.org/R") install.packages("FLXSA", repos="http://flr-project.org/R") @@ -44,8 +66,7 @@ Ajouter dans les script csh:: - setenv R_HOME /home3/caparmor/poussin/R/lib64/R - setenv PATH ${R_HOME}/bin:${PATH} + setenv R_HOME /appli/R/2.15.0-gnu-4.3/lib64/R setenv LD_LIBRARY_PATH ${R_HOME}/lib Et lancer les simulations avec tous les composants en 64 bits Modified: branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/launcher/SshSimulatorLauncherTest.java =================================================================== --- branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/launcher/SshSimulatorLauncherTest.java 2012-05-11 12:05:56 UTC (rev 3698) +++ branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/launcher/SshSimulatorLauncherTest.java 2012-05-14 09:53:20 UTC (rev 3699) @@ -315,7 +315,7 @@ } /** - * Test que les ${PATH} et ${R_HOME} ne sont pas interpreté par freemarker. + * Test que ${R_HOME} n'est pas interpreté par freemarker. * * @throws IOException * @throws TemplateException @@ -326,8 +326,7 @@ String content = launcher.getSimulationScriptLaunchContent( SSHSimulatorLauncher.QSUB_SCRIPT_TEMPLATE, "", "", true, "", "", true); - System.out.println(content); - Assert.assertTrue(content.contains("${R_HOME}/bin:${PATH}")); + Assert.assertTrue(content.contains("${R_HOME}/lib")); } } \ No newline at end of file