July 2014 - Isis-fish-commits - mailman.cloud.codelutin.com

r4044 - trunk/src/main/java/fr/ifremer/isisfish/aspect
by echatellier＠users.forge.codelutin.com July 19, 2014

July 19, 2014

Author: echatellier Date: 2014-07-19 12:11:28 +0200 (Sat, 19 Jul 2014) New Revision: 4044 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4044 Log: Ajout de commentaire sur les aspects aspectj Modified: trunk/src/main/java/fr/ifremer/isisfish/aspect/AspectJUrlClassLoader.java trunk/src/main/java/fr/ifremer/isisfish/aspect/AspectJWeavingAdaptor.java Modified: trunk/src/main/java/fr/ifremer/isisfish/aspect/AspectJUrlClassLoader.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/aspect/AspectJUrlClassLoader.java 2014-07-19 08:52:22 UTC (rev 4043) +++ trunk/src/main/java/fr/ifremer/isisfish/aspect/AspectJUrlClassLoader.java 2014-07-19 10:11:28 UTC (rev 4044) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2013 Ifremer, Code Lutin, Chatellier Eric + * Copyright (C) 2013 - 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 @@ -37,6 +37,18 @@ import org.aspectj.weaver.tools.TraceFactory; import org.aspectj.weaver.tools.WeavingClassLoader; +/** + * Cette classe est un copié/coller de {@link org.aspectj.weaver.loadtime.WeavingURLClassLoader} qui permet de définit + * notre propre instance de {@code adaptor} pour, dans le cas d'IsisFish, permettre d'ajouter des aspects à l'execution. + * + * Elle définie deux nouvelles méthodes: + * <ul> + * <li>{@link #deploy(Class)} : qui permet de deployer un nouvel aspect<li> + * <li>{@link #prepare()} : à appeler après l'ajout de tous les aspects dynamiques</li> + * </ul> + * + * @since 4.2.0.0 + */ public class AspectJUrlClassLoader extends ExtensibleURLClassLoader implements WeavingClassLoader { public static final String WEAVING_CLASS_PATH = "aj.class.path"; Modified: trunk/src/main/java/fr/ifremer/isisfish/aspect/AspectJWeavingAdaptor.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/aspect/AspectJWeavingAdaptor.java 2014-07-19 08:52:22 UTC (rev 4043) +++ trunk/src/main/java/fr/ifremer/isisfish/aspect/AspectJWeavingAdaptor.java 2014-07-19 10:11:28 UTC (rev 4044) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2013 Ifremer, Code Lutin, Chatellier Eric + * Copyright (C) 2013 - 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 @@ -33,6 +33,7 @@ import java.util.Iterator; import java.util.List; +import org.apache.commons.io.IOUtils; import org.aspectj.apache.bcel.classfile.ClassParser; import org.aspectj.apache.bcel.classfile.JavaClass; import org.aspectj.bridge.IMessageHandler; @@ -52,6 +53,24 @@ import org.aspectj.weaver.tools.cache.SimpleCache; import org.aspectj.weaver.tools.cache.SimpleCacheFactory; +/** + * Cette classe étend {@link WeavingAdaptor} pour avoir une instance personnalisée du champ {@link #weaver}. + * + * Toutes la logique consiste ensuite à pouvoir appeler le code {@code weaver.weave(wcp);} pour pouvoir déployer un + * apect à l'execution dans le {@code weaver} qui servira ensuite à "aspectiser une classe" via la méthode + * {@link #weaveClass(String, byte[])}. + * + * Elle utilise pour l'instant de l'introspection agressive pour acceder aux attributs privés de la classe parentes et + * les rendre visible. + * + * TODO : au lieu d'ajouter à la demande des aspects, on pourrait les ajouters en parmanence, mais en les activant de + * facon conditionnelle (if() cutpoint). + * A tester. Il est possible que sans le cas d'isis, une classe non aspectisée soit plus performante qu'une classe + * dont les aspects ne sont pas activés. + * Voir la discussion : http://aspectj.2085585.n4.nabble.com/Runtime-weaving-without-agent-tp465083… + * + * @since 4.2.0.0 + */ public class AspectJWeavingAdaptor extends WeavingAdaptor { protected ClassLoader parentLoader; @@ -115,9 +134,10 @@ public byte[] deploy(Class<?> aspectClass) { byte[] result = null; + InputStream is = null; try { String name = aspectClass.getName(); - InputStream is = AspectJWeavingAdaptor.class.getResourceAsStream("/" + name.replace('.', '/') + ".class"); + is = AspectJWeavingAdaptor.class.getResourceAsStream("/" + name.replace('.', '/') + ".class"); byte[] bytes = FileUtil.readAsByteArray(is); is.close(); ClassParser parser = new ClassParser(new ByteArrayInputStream(bytes), name); @@ -134,6 +154,8 @@ } catch (IOException e) { throw new RuntimeException("Can't create aspect", e); + } finally { + IOUtils.closeQuietly(is); } return result;

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r4043 - branches
by echatellier＠users.forge.codelutin.com July 19, 2014

July 19, 2014

Author: echatellier Date: 2014-07-19 10:52:22 +0200 (Sat, 19 Jul 2014) New Revision: 4043 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4043 Log: Remove unused branches Removed: branches/3.0.20/ branches/3.1.3/ branches/3.1.4/ branches/3.2.0.5.x/ branches/3.2.1/ branches/3.3.0.4-disworksupport/ branches/3.3.1/ branches/4.0.0-svnkit/ branches/4.0.1/ branches/4.1/ branches/arbo-maven/ branches/codelutin/ branches/isis-fish-3.2.0.8/ branches/isis-fish-3.3.0.x/ branches/maven2_multimodule/ branches/multi-thread-worker/ branches/svn/

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r4042 - trunk/src/main/java/fr/ifremer/isisfish/util
by bpoussin＠users.forge.codelutin.com July 18, 2014

July 18, 2014

Author: bpoussin Date: 2014-07-18 20:20:13 +0200 (Fri, 18 Jul 2014) New Revision: 4042 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4042 Log: default to 1.3 to resize cache (before 3) Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java 2014-07-17 17:27:13 UTC (rev 4041) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java 2014-07-18 18:20:13 UTC (rev 4042) @@ -59,7 +59,7 @@ /** number of time steps to cache by interpolating from the first step*/ // perhaps allow the configuration - static public int CACHE_STEP = 3; + static public double CACHE_STEP = 1.3; // between 2 step, cache size is very close: 1.3 seem correct static public class IsisCacheBackendOnGuavaFactory implements IsisCacheBackend.Factory { @Override @@ -256,7 +256,7 @@ // after first step, use information to resize cache if (!adjusted) { - adjustedCache(stepAmount * CACHE_STEP); // keep place for 3 step + adjustedCache((long)(stepAmount * CACHE_STEP)); // keep place for 1.3 step adjusted = true; } }

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r4041 - in trunk/src/main: java/fr/ifremer/isisfish/simulator java/fr/ifremer/isisfish/simulator/launcher resources/i18n
by bpoussin＠users.forge.codelutin.com July 17, 2014

July 17, 2014

Author: bpoussin Date: 2014-07-17 19:27:13 +0200 (Thu, 17 Jul 2014) New Revision: 4041 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4041 Log: add remaining time in progress bar Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationControl.java trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationServiceTableModel.java 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/simulator/SimulationContext.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-07-17 16:04:09 UTC (rev 4040) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-07-17 17:27:13 UTC (rev 4041) @@ -44,11 +44,12 @@ import fr.ifremer.isisfish.util.IsisCache; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; -//import fr.ifremer.isisfish.util.Trace; import org.nuiton.config.ApplicationConfig; import org.nuiton.config.OverwriteApplicationConfig; import org.nuiton.math.matrix.MatrixFactory; +import org.nuiton.profiling.Statistic; import org.nuiton.profiling.Trace; +import org.nuiton.profiling.Unit; /** * Keep all information on one simulation. @@ -87,10 +88,40 @@ protected PropertyChangeListener stepListener = new PropertyChangeListener() { @Override public void propertyChange(PropertyChangeEvent evt) { - SimulationContext.this.fireStepChange(new TimeStep((Integer)evt.getNewValue())); + Integer i = (Integer)evt.getNewValue(); + SimulationContext.this.fireStepChange(new TimeStep(i)); + + // met a jour les stats sur le temps des pas de temps + Statistic stat = SimulationContext.this.timeStepStat; + stat.add(i); + SimulationContext.this.getSimulationControl().setTimeStepMeanTime( + Unit.Time.nano.convertTo(Unit.Time.s, stat.getMean())); } }; + protected Statistic timeStepStat = new Statistic("Step time"){ + protected long lastTime = 0; + // add delta not value + @Override + public void add(long value) { + if (lastTime == 0) { + lastTime = System.nanoTime(); + } else { + long newTime = System.nanoTime(); + long delta = newTime - lastTime; + lastTime = newTime; + super.add(delta); + } + + } + + @Override + public String formatValue(long value) { + String result = String.valueOf(Unit.Time.nano.convertTo(Unit.Time.s, value)); + return result; + } + }; + protected ClassLoader classLoader = null; protected File scriptDirectory; /** l'objet trace qui conserve les donnees statistiques des appels de methodes */ @@ -311,6 +342,10 @@ this.simulation = simulation; } + public Statistic getTimeStepStat() { + return timeStepStat; + } + /** * @return Returns the simulationControl. */ Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationControl.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationControl.java 2014-07-17 16:04:09 UTC (rev 4040) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationControl.java 2014-07-17 17:27:13 UTC (rev 4041) @@ -65,6 +65,8 @@ protected long progressMax = 0; protected long progress = 0; protected String text = ""; + // temps moyen d'un pas de temps vaut 0 tant que pas mis a jour + protected double timeStepMeanTime; /** Control save mecanism each time a property is changed (default to false). */ protected transient boolean autoSaveState = false; @@ -303,6 +305,25 @@ } /** + * Set mean time for one step in second + * @param timeStepMeanTime + */ + public void setTimeStepMeanTime(double timeStepMeanTime) { + double oldValue = this.timeStepMeanTime; + this.timeStepMeanTime = timeStepMeanTime; + listeners.firePropertyChange("timeStepMeanTime", oldValue, this.timeStepMeanTime); + } + + /** + * Get mean time for one step in second + * @return + */ + public double getTimeStepMeanTime() { + return timeStepMeanTime; + } + + + /** * Met dans un Properties tous les champs * @return un Properties avec tous les champs */ @@ -318,6 +339,7 @@ result.setProperty("progressMax", String.valueOf(progressMax)); result.setProperty("progress", String.valueOf(progress)); result.setProperty("text", text); + result.setProperty("timeStepMeanTime", String.valueOf(timeStepMeanTime)); return result; } @@ -371,6 +393,10 @@ String text = props.getProperty("text"); setText(text); } + if (props.containsKey("timeStepMeanTime")) { + double timeStepMeanTime = Double.parseDouble(props.getProperty("timeStepMeanTime")); + setTimeStepMeanTime(timeStepMeanTime); + } } finally { inUpdateFromProperties = false; } Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2014-07-17 16:04:09 UTC (rev 4040) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2014-07-17 17:27:13 UTC (rev 4041) @@ -71,8 +71,6 @@ import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.CompileHelper; import org.nuiton.math.matrix.MatrixFactory; -import org.nuiton.profiling.Statistic; -import org.nuiton.profiling.Unit; /** * Fait une simulation dans la meme jvm. @@ -89,46 +87,8 @@ private static Log log = LogFactory .getLog(InProcessSimulatorLauncher.class); - protected static class StepTimeStat implements SimulationListener { - - protected long lastTime = 0; - protected Statistic stat = new Statistic("Step time"){ - @Override - public String formatValue(long value) { - String result = String.valueOf(Unit.Time.nano.convertTo(Unit.Time.s, value)); - return result; - } - }; - - public Statistic getStat() { - return stat; - } - - @Override - public void beforeSimulation(SimulationContext context) { - } - - @Override - public void stepChange(SimulationContext context, TimeStep step) { - if (lastTime == 0) { - lastTime = System.nanoTime(); - } else { - long newTime = System.nanoTime(); - long delta = newTime - lastTime; - lastTime = newTime; - stat.add(delta); - } - } - - @Override - public void afterSimulation(SimulationContext context) { - } - - } - protected SimulationStorage simulation; - protected StepTimeStat stepTimeStat = new StepTimeStat(); - + /** * {@inheritDoc} */ @@ -475,7 +435,7 @@ simulatorObject.simulate(context); simulation.getInformation().addInformation( - stepTimeStat.getStat().exportText(null).toString()); + context.getTimeStepStat().exportText(null).toString()); // // Ajout des nouveaux objets créés durant la simulation @@ -588,9 +548,6 @@ // - ResultStorage context.addSimulationListener(simulation.getResultStorage()); - // ajout du listener de statistique sur le temps de chaque pas de temps - context.addSimulationListener(stepTimeStat); - // - TODO: mexico xml result // - TODO: vle result String simListener = context.getSimulationStorage().getParameter() Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationServiceTableModel.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationServiceTableModel.java 2014-07-17 16:04:09 UTC (rev 4040) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationServiceTableModel.java 2014-07-17 17:27:13 UTC (rev 4041) @@ -43,6 +43,8 @@ import fr.ifremer.isisfish.simulator.SimulationControl; import fr.ifremer.isisfish.simulator.SimulationParameter; import fr.ifremer.isisfish.types.TimeStep; +import org.apache.commons.lang3.time.DurationFormatUtils; +import org.nuiton.profiling.Unit; /** * Model de table pour suivre l'evolution des differentes simulations en cours. @@ -266,13 +268,25 @@ break; case 4: JProgressBar pb = getProgressBar(job); - pb.setMaximum((int) control.getProgressMax()); - pb.setValue((int) control.getProgress()); + int value = (int) control.getProgress(); + int max = (int) control.getProgressMax(); + + String restTime = ""; + int rest = max - value; + double time = rest * control.getTimeStepMeanTime(); + if (time > 0) { + long milli = (long)Unit.Time.s.convertTo(Unit.Time.milli, time); + restTime = DurationFormatUtils.formatDurationHMS(milli); + } + + pb.setMaximum(max); + pb.setValue(value); + // progress can be used for other things TimeStep step = control.getStep(); if (step != null) { - pb.setString(step.getMonth() + "/" + step.getYear()); + pb.setString(step.getMonth() + "/" + step.getYear() + " ("+ restTime +")"); } else { pb.setString(""); @@ -329,6 +343,7 @@ setData(); } + @Override public void setData() { ArrayList<SimulationJob> jobs = new ArrayList<SimulationJob>(simulationService.getJobs()); for (SimulationJob job : jobs) { @@ -338,6 +353,7 @@ model.setJobs(jobs); } + @Override public void simulationStart(SimulationService simService, SimulationJob job) { model.addJob(job); @@ -345,6 +361,7 @@ model.controlListener); } + @Override public void simulationStop(SimulationService simService, SimulationJob job) { model.removeJob(job); @@ -352,6 +369,7 @@ model.controlListener); } + @Override public void clearJobDone(SimulationService simService) { // nothing to do } Modified: trunk/src/main/resources/i18n/isis-fish_en_GB.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2014-07-17 16:04:09 UTC (rev 4040) +++ trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2014-07-17 17:27:13 UTC (rev 4041) @@ -531,7 +531,7 @@ isisfish.input.tree.strategies=Strategies isisfish.input.tree.triptypes=Trip types isisfish.input.tree.vesseltypes=Vessel types -isisfish.input.tree.zones=Zones +isisfish.input.tree.zones= isisfish.launch.anonymous=read only isisfish.launch.email=email isisfish.launch.firstname=firstname @@ -722,14 +722,14 @@ isisfish.population.capturability=Capturability isisfish.population.comments=Comments isisfish.population.group=Group -isisfish.population.groups=Groups +isisfish.population.groups= isisfish.population.mappingZoneReproZoneRecru=MappingZoneReproZoneRecru isisfish.population.matrixAbundance=Abundance matrix isisfish.population.matrixAbundance1D=matrixAbundance1D isisfish.population.recruitment=Recruitment isisfish.population.reproduction=Reproduction isisfish.population.season=Season -isisfish.population.zones=Zones +isisfish.population.zones= isisfish.populationBasics.confirmCreateGroups=Warning, running groups creation wizard will delete all existing groups and objects which depend on it.\nDo you want to re-create groups ? isisfish.populationBasics.geographicID=Geographic identifier isisfish.populationBasics.groupMax=Max group @@ -762,7 +762,7 @@ isisfish.populationGroup.naturalDeathRate=Natural death rate isisfish.populationGroup.price=Price isisfish.populationGroup.reproductionRate=Reproduction rate -isisfish.populationGroup.title=Groups +isisfish.populationGroup.title= isisfish.populationGroup.toString=%1$s Group %2$s isisfish.populationMigration.comments=Comments isisfish.populationMigration.selectSeason=Select a season @@ -808,7 +808,7 @@ isisfish.populationZones.selectPopulationAreas=Select the population areas isisfish.populationZones.selectRecruitmentAreas=Select the recruitment areas isisfish.populationZones.selectSpawningAreas=Select the spawning areas -isisfish.populationZones.title=Zones +isisfish.populationZones.title= isisfish.port.cell=Port cell isisfish.port.comments=Comments isisfish.port.name=Name Modified: trunk/src/main/resources/i18n/isis-fish_fr_FR.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2014-07-17 16:04:09 UTC (rev 4040) +++ trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2014-07-17 17:27:13 UTC (rev 4041) @@ -531,7 +531,7 @@ isisfish.input.tree.strategies=Stratégies isisfish.input.tree.triptypes=Types de marée isisfish.input.tree.vesseltypes=Types de navire -isisfish.input.tree.zones=Zones +isisfish.input.tree.zones= isisfish.launch.anonymous=lecture seule isisfish.launch.email=courriel isisfish.launch.firstname=nom @@ -724,7 +724,7 @@ isisfish.population.recruitment=Recrutement isisfish.population.reproduction=Reproduction isisfish.population.season=Saison -isisfish.population.zones=Zones +isisfish.population.zones= isisfish.populationBasics.confirmCreateGroups=Attention, la re-création des groupes supprimera les groupes existants et tous les objets qui en dépendent.\nÊtes vous sur de vouloir re-créer les groupes ? isisfish.populationBasics.geographicID=Identifiant géographique isisfish.populationBasics.groupMax=Group max @@ -803,7 +803,7 @@ isisfish.populationZones.selectPopulationAreas=Sélectionnez les zones des populations isisfish.populationZones.selectRecruitmentAreas=Sélectionnez les zones de recrutement isisfish.populationZones.selectSpawningAreas=Sélectionnez les zones de reproduction -isisfish.populationZones.title=Zones +isisfish.populationZones.title= isisfish.port.cell=Maille du port isisfish.port.comments=Commentaires isisfish.port.name=Nom

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r4040 - in trunk/src/main: java/fr/ifremer/isisfish/datastore resources/i18n
by bpoussin＠users.forge.codelutin.com July 17, 2014

July 17, 2014

Author: bpoussin Date: 2014-07-17 18:04:09 +0200 (Thu, 17 Jul 2014) New Revision: 4040 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4040 Log: better info message Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java 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/datastore/ResultStorageCSV.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java 2014-07-16 20:45:26 UTC (rev 4039) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java 2014-07-17 16:04:09 UTC (rev 4040) @@ -148,14 +148,20 @@ @Override public String getInfo() { + String oldest = ""; + if (maxGapWithCurrentStepReadOnDisk > 0) { + oldest = String.format("\tthe oldest step read on disk was %s step before current step\n", + maxGapWithCurrentStepReadOnDisk); + } + return String.format( "ResultStorageCSV:\n" + "\t%s results written to disk on a total of %s\n" + "\t%s results read (%s in cache and %s on disk)\n" - + "\tthe oldest step read on disk was %s step before current step\n", + + "%s", numberOfResultOnDisk, numberOfResult, numberOfResultAsked, numberOfResultReadInCache, numberOfResultReadOnDisk, - maxGapWithCurrentStepReadOnDisk); + oldest); } /** Modified: trunk/src/main/resources/i18n/isis-fish_en_GB.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2014-07-16 20:45:26 UTC (rev 4039) +++ trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2014-07-17 16:04:09 UTC (rev 4040) @@ -29,6 +29,7 @@ Error\ during\ vcs\ initialisation= Error\ while\ uploading\ public\ key\ to\ remote\ serveur\ authorized_keys= Generate\ next\ simulation= +Groups= Import\ one\ java\ file\ script\ source= Import\ simulation\ file\ %s\ in\ directory\ %s\ and\ rename\ from\ %s\ to\ %s= Import\ zipped\ file\ containing\ all\ scripts\ directory\ structure= @@ -68,6 +69,7 @@ Use\ branches,\ switch\ not\ needed= User\ restart\ simulation\ %s= User\ stop\ simulation\ %s= +Zones= an\ alternative\ way\ to\ specify\ the\ scale.= could\ not\ close\ reader\ %1$s=could not close reader %1$s could\ not\ found\ %s= Modified: trunk/src/main/resources/i18n/isis-fish_fr_FR.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2014-07-16 20:45:26 UTC (rev 4039) +++ trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2014-07-17 16:04:09 UTC (rev 4040) @@ -29,6 +29,7 @@ Error\ during\ vcs\ initialisation= Error\ while\ uploading\ public\ key\ to\ remote\ serveur\ authorized_keys= Generate\ next\ simulation= +Groups= Import\ one\ java\ file\ script\ source= Import\ simulation\ file\ %s\ in\ directory\ %s\ and\ rename\ from\ %s\ to\ %s= Import\ zipped\ file\ containing\ all\ scripts\ directory\ structure= @@ -68,6 +69,7 @@ Use\ branches,\ switch\ not\ needed= User\ restart\ simulation\ %s= User\ stop\ simulation\ %s= +Zones= an\ alternative\ way\ to\ specify\ the\ scale.= could\ not\ close\ reader\ %1$s=could not close reader %1$s could\ not\ found\ %s=

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r4039 - trunk/src/main/java/fr/ifremer/isisfish/simulator
by bpoussin＠users.forge.codelutin.com July 16, 2014

July 16, 2014

Author: bpoussin Date: 2014-07-16 22:45:26 +0200 (Wed, 16 Jul 2014) New Revision: 4039 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4039 Log: add dimension name in initial N Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationParameterImpl.java Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationParameterImpl.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationParameterImpl.java 2014-07-11 15:35:04 UTC (rev 4038) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationParameterImpl.java 2014-07-16 20:45:26 UTC (rev 4039) @@ -76,6 +76,8 @@ import fr.ifremer.isisfish.rule.RuleHelper; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityAnalysis; +import static org.nuiton.i18n.I18n.n; + /** * Real {@link SimulationParameter} implementation. * @@ -315,7 +317,10 @@ zones.add("No zone"); } List[] semantics = new List[] { groups, zones }; - result = MatrixFactory.getInstance().create(semantics); + result = MatrixFactory.getInstance().create( + n("matrixAbundance"), + semantics, + new String[] { n("Groups"), n("Zones") }); numbers.put(pop, result); }

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r4038 - in trunk: . src/license src/main/java/fr/ifremer/isisfish/datastore src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard src/main/java/fr/ifremer/isisfish/util
by bpoussin＠users.forge.codelutin.com July 11, 2014

July 11, 2014

Author: bpoussin Date: 2014-07-11 17:35:04 +0200 (Fri, 11 Jul 2014) New Revision: 4038 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4038 Log: - add license header - use nuiton-matrix 2.5-SNAPSHOT Modified: trunk/pom.xml trunk/src/license/THIRD-PARTY.properties trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/ContinuousDistributionPanel.java trunk/src/main/java/fr/ifremer/isisfish/util/SimpleParser.java Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-07-11 11:21:35 UTC (rev 4037) +++ trunk/pom.xml 2014-07-11 15:35:04 UTC (rev 4038) @@ -88,14 +88,14 @@ <dependency> <groupId>org.nuiton.matrix</groupId> <artifactId>nuiton-matrix</artifactId> - <version>2.4.2-SNAPSHOT</version> + <version>2.5-SNAPSHOT</version> <scope>compile</scope> </dependency> <dependency> <groupId>org.nuiton.matrix</groupId> <artifactId>nuiton-matrix-gui</artifactId> - <version>2.4.2-SNAPSHOT</version> + <version>2.5-SNAPSHOT</version> <scope>compile</scope> </dependency> Modified: trunk/src/license/THIRD-PARTY.properties =================================================================== --- trunk/src/license/THIRD-PARTY.properties 2014-07-11 11:21:35 UTC (rev 4037) +++ trunk/src/license/THIRD-PARTY.properties 2014-07-11 15:35:04 UTC (rev 4038) @@ -45,9 +45,8 @@ # Please fill the missing licenses for dependencies : # # -#Fri May 30 10:59:27 CEST 2014 +#Fri Jul 11 17:44:59 CEST 2014 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 -javax.activation--activation--1.1.1=COMMON DEVELOPMENT AND DISTRIBUTION LICENSE (CDDL) Version 1.0 org.antlr--antlr-runtime--3.4=BSD License Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java 2014-07-11 11:21:35 UTC (rev 4037) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java 2014-07-11 15:35:04 UTC (rev 4038) @@ -1,6 +1,28 @@ package fr.ifremer.isisfish.datastore; +/* + * #%L + * IsisFish + * %% + * Copyright (C) 1999 - 2014 Ifremer, Codelutin + * %% + * 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% + */ + import fr.ifremer.isisfish.IsisFish; import fr.ifremer.isisfish.IsisFishRuntimeException; import fr.ifremer.isisfish.simulator.SimulationContext; 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 2014-07-11 11:21:35 UTC (rev 4037) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/ContinuousDistributionPanel.java 2014-07-11 15:35:04 UTC (rev 4038) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2012, 2014 Ifremer, Codelutin, Chatellier Eric + * Copyright (C) 2012 - 2014 Ifremer, Codelutin, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as Modified: trunk/src/main/java/fr/ifremer/isisfish/util/SimpleParser.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/SimpleParser.java 2014-07-11 11:21:35 UTC (rev 4037) +++ trunk/src/main/java/fr/ifremer/isisfish/util/SimpleParser.java 2014-07-11 15:35:04 UTC (rev 4038) @@ -1,6 +1,28 @@ package fr.ifremer.isisfish.util; +/* + * #%L + * IsisFish + * %% + * Copyright (C) 1999 - 2014 Ifremer, Codelutin + * %% + * 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% + */ + import java.io.BufferedReader; import java.io.IOException; import org.apache.commons.logging.Log;

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r4037 - in trunk/src/main: java/fr/ifremer/isisfish java/fr/ifremer/isisfish/simulator java/fr/ifremer/isisfish/ui resources/i18n
by bpoussin＠users.forge.codelutin.com July 11, 2014

July 11, 2014

Author: bpoussin Date: 2014-07-11 13:21:35 +0200 (Fri, 11 Jul 2014) New Revision: 4037 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4037 Log: - can use Lazy or not via configuration Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java 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/IsisConfig.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-07-11 08:50:40 UTC (rev 4036) +++ trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-07-11 11:21:35 UTC (rev 4037) @@ -846,6 +846,8 @@ getOption(Option.SIMULATION_MATRIX_VECTOR_SPARSE_CLASS.key)); result.put(Option.SIMULATION_MATRIX_THRESHOLD_USE_SPARSE_CLASS.key, getOption(Option.SIMULATION_MATRIX_THRESHOLD_USE_SPARSE_CLASS.key)); + result.put(Option.SIMULATION_MATRIX_USE_LAZY_VECTOR.key, + getOption(Option.SIMULATION_MATRIX_USE_LAZY_VECTOR.key)); result.put(Option.SIMULATION_STORE_RESULT_ON_DISK.key, getOption(Option.SIMULATION_STORE_RESULT_ON_DISK.key)); result.put(Option.SIMULATION_STORE_RESULT_CACHE_STEP.key, @@ -1010,6 +1012,18 @@ } /** + * Seuil d'uitilisation des matrices creuse + * + * @return + * @since 4.3.1.0 + */ + public boolean getSimulationMatrixdUseLazyVector() { + ApplicationConfig config = SimulationContext.get().getConfig(); + boolean result = config.getOptionAsBoolean(Option.SIMULATION_MATRIX_USE_LAZY_VECTOR.key); + return result; + } + + /** * Indique le nombre de pas qui doivent etre sauve, en partant du dernier pas * de temps. * @@ -1083,6 +1097,7 @@ SIMULATION_MATRIX_VECTOR_CLASS("simulation.matrix.vector.class", n("isisfish.config.simulation.matrix.vector.class.description"), DoubleBigVector.class.getName()), SIMULATION_MATRIX_VECTOR_SPARSE_CLASS("simulation.matrix.vector.sparse.class", n("isisfish.config.simulation.matrix.vector.sparse.class.description"), DoubleSparseHashVector.class.getName()), SIMULATION_MATRIX_THRESHOLD_USE_SPARSE_CLASS("simulation.matrix.threshold.use.sparse.class", n("isisfish.config.simulation.matrix.threshold.use.sparse.class.description"), "1000"), + SIMULATION_MATRIX_USE_LAZY_VECTOR("simulation.matrix.use.lazy.vector", n("isisfish.config.simulation.matrix.use.lazy.vector.description"), "true"), SIMULATION_STORE_RESULT_ON_DISK("simulation.store.result.ondisk", n("isisfish.config.simulation.store.result.ondisk.description"), "-1"), SIMULATION_STORE_RESULT_CACHE_STEP("simulation.store.result.cachestep", n("isisfish.config.simulation.store.result.cachestep.description"), "13"), Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-07-11 08:50:40 UTC (rev 4036) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-07-11 11:21:35 UTC (rev 4037) @@ -131,7 +131,8 @@ MatrixFactory.initMatrixFactoryThreadLocal( IsisFish.config.getSimulationMatrixVectorClass(), IsisFish.config.getSimulationMatrixVectorSparseClass(), - IsisFish.config.getSimulationMatrixThresholdUseSparse()); + IsisFish.config.getSimulationMatrixThresholdUseSparse(), + IsisFish.config.getSimulationMatrixdUseLazyVector()); } /** Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java 2014-07-11 08:50:40 UTC (rev 4036) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java 2014-07-11 11:21:35 UTC (rev 4037) @@ -228,6 +228,7 @@ modelBuilder.addOption(IsisConfig.Option.SIMULATION_MATRIX_VECTOR_CLASS); modelBuilder.addOption(IsisConfig.Option.SIMULATION_MATRIX_VECTOR_SPARSE_CLASS); modelBuilder.addOption(IsisConfig.Option.SIMULATION_MATRIX_THRESHOLD_USE_SPARSE_CLASS); + modelBuilder.addOption(IsisConfig.Option.SIMULATION_MATRIX_USE_LAZY_VECTOR); modelBuilder.addOption(IsisConfig.Option.MAPPED_RESULT_MATRIX_VECTOR_CLASS); modelBuilder.addOption(IsisConfig.Option.SIMULATION_STORE_RESULT_ON_DISK); modelBuilder.addOption(IsisConfig.Option.SIMULATION_STORE_RESULT_CACHE_STEP); Modified: trunk/src/main/resources/i18n/isis-fish_en_GB.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2014-07-11 08:50:40 UTC (rev 4036) +++ trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2014-07-11 11:21:35 UTC (rev 4037) @@ -230,6 +230,7 @@ isisfish.config.main.userName.description=User name isisfish.config.mapped.result.matrix.vector.class.description= isisfish.config.simulation.matrix.threshold.use.sparse.class.description= +isisfish.config.simulation.matrix.use.lazy.vector.description= isisfish.config.simulation.matrix.vector.class.description= isisfish.config.simulation.matrix.vector.sparse.class.description= isisfish.config.simulation.store.result.cachestep.description= Modified: trunk/src/main/resources/i18n/isis-fish_fr_FR.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2014-07-11 08:50:40 UTC (rev 4036) +++ trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2014-07-11 11:21:35 UTC (rev 4037) @@ -230,6 +230,7 @@ isisfish.config.main.userName.description=le nom - prénom de l'utilisateur isisfish.config.mapped.result.matrix.vector.class.description= isisfish.config.simulation.matrix.threshold.use.sparse.class.description= +isisfish.config.simulation.matrix.use.lazy.vector.description= isisfish.config.simulation.matrix.vector.class.description= isisfish.config.simulation.matrix.vector.sparse.class.description= isisfish.config.simulation.store.result.cachestep.description=

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r4036 - trunk
by echatellier＠users.forge.codelutin.com July 11, 2014

July 11, 2014

Author: echatellier Date: 2014-07-11 10:50:40 +0200 (Fri, 11 Jul 2014) New Revision: 4036 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4036 Log: Update libs Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-07-10 23:17:57 UTC (rev 4035) +++ trunk/pom.xml 2014-07-11 08:50:40 UTC (rev 4036) @@ -20,7 +20,7 @@ <dependency> <groupId>org.nuiton</groupId> <artifactId>nuiton-utils</artifactId> - <version>3.0-rc-3</version> + <version>3.0-rc-4</version> <scope>compile</scope> </dependency> @@ -290,7 +290,7 @@ <dependency> <groupId>org.aspectj</groupId> <artifactId>aspectjweaver</artifactId> - <version>1.8.0</version> + <version>1.8.1</version> </dependency> <dependency> @@ -312,7 +312,7 @@ <dependency> <groupId>org.tmatesoft.svnkit</groupId> <artifactId>svnkit</artifactId> - <version>1.8.3-1</version> + <version>1.8.5</version> <scope>compile</scope> </dependency>  @@ -327,7 +327,7 @@ <dependency> <groupId>org.eclipse.jdt.core.compiler</groupId> <artifactId>ecj</artifactId> - <version>4.3.1</version> + <version>4.4</version> </dependency> <dependency> @@ -483,7 +483,7 @@  <jaxxVersion>2.8.7</jaxxVersion> <eugeneVersion>2.7.4</eugeneVersion> - <topiaVersion>2.9-rc-1</topiaVersion> + <topiaVersion>2.9.1</topiaVersion> <hibernateVersion>4.3.5.Final</hibernateVersion> <nuitonI18nVersion>3.1</nuitonI18nVersion> <nuitonWidgetsVersion>1.1.1</nuitonWidgetsVersion>

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r4035 - trunk/src/main/java/fr/ifremer/isisfish/util
by bpoussin＠users.forge.codelutin.com July 10, 2014

July 10, 2014

Author: bpoussin Date: 2014-07-11 01:17:57 +0200 (Fri, 11 Jul 2014) New Revision: 4035 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4035 Log: remove old code Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java 2014-07-10 16:41:47 UTC (rev 4034) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java 2014-07-10 23:17:57 UTC (rev 4035) @@ -109,7 +109,7 @@ Object result; - if (Void.TYPE == method.getReturnType()) { + if (Void.TYPE.equals(method.getReturnType())) { // for void return type, never put it in cache, we can call directly real method result = realCall(defaultValue); } else { @@ -140,16 +140,10 @@ String key = sbKey.toString().intern(); result = get(step, key); if (result == null) { - - // computation increment (/ by 0) - // FIXME need to be called, but fail with empty stack - //getTrace().traceAfterComputation(method); result = realCall(defaultValue); // si return null on stock NULL pour faire la distinction // entre present dans le cache ou absent (get(...) return null) -// if (returnType != != null) { // util pour les methodes retournant void, ne fonctionne pas si on met AND !execute(void *(..)) dans l'aspect. En fait fonction seulement si utilisé avec les traces :( put(step, key, result==null?NULL:result); -// } } else { if (result == NULL) { result = null;

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