October 2014 - Isis-fish-data-commits - mailman.cloud.codelutin.com

r346 - in tags/4.3.1: scripts simulators
by echatellier＠users.forge.codelutin.com 08 Oct '14

08 Oct '14

Author: echatellier Date: 2014-10-08 13:13:07 +0200 (Wed, 08 Oct 2014) New Revision: 346 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/346 Log: Use result manager Modified: tags/4.3.1/scripts/SiMatrix.java tags/4.3.1/simulators/DefaultSimulator.java Modified: tags/4.3.1/scripts/SiMatrix.java =================================================================== --- tags/4.3.1/scripts/SiMatrix.java 2014-10-08 11:00:58 UTC (rev 345) +++ tags/4.3.1/scripts/SiMatrix.java 2014-10-08 11:13:07 UTC (rev 346) @@ -55,10 +55,10 @@ import fr.ifremer.isisfish.entities.StrategyMonthInfo; import fr.ifremer.isisfish.entities.Zone; import fr.ifremer.isisfish.entities.ZoneDAO; +import fr.ifremer.isisfish.simulator.ResultManager; import fr.ifremer.isisfish.simulator.SimulationContext; +import fr.ifremer.isisfish.types.Month; import fr.ifremer.isisfish.types.TimeStep; -import fr.ifremer.isisfish.types.Month; -import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.util.Nocache; /** @@ -1891,7 +1891,7 @@ * @param pop population * @return Fishing mortality per group per year (computed in December) */ - public MatrixND fishingMortalityPerGroup(TimeStep step, Population pop, ResultStorage resManager) throws TopiaException { + public MatrixND fishingMortalityPerGroup(TimeStep step, Population pop, ResultManager resManager) throws TopiaException { double Fgroup = 0; double Cgroup = 0; double Mgroup = 0; Modified: tags/4.3.1/simulators/DefaultSimulator.java =================================================================== --- tags/4.3.1/simulators/DefaultSimulator.java 2014-10-08 11:00:58 UTC (rev 345) +++ tags/4.3.1/simulators/DefaultSimulator.java 2014-10-08 11:13:07 UTC (rev 346) @@ -499,7 +499,7 @@ if (resManager.isEnabled(ResultName.MATRIX_FISHING_MORTALITY_PER_GROUP) || resManager.isEnabled(ResultName.MATRIX_TOTAL_FISHING_MORTALITY)) { MatrixND fishingMortalityPerGroup = siMatrix.fishingMortalityPerGroup(step, - pop, context.getSimulationStorage().getResultStorage()); + pop, context.getResultManager()); if (resManager.isEnabled(ResultName.MATRIX_FISHING_MORTALITY_PER_GROUP)) { resManager.addResult(step, pop, fishingMortalityPerGroup);

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r345 - in trunk: scripts simulators
by echatellier＠users.forge.codelutin.com 08 Oct '14

08 Oct '14

Author: echatellier Date: 2014-10-08 13:00:58 +0200 (Wed, 08 Oct 2014) New Revision: 345 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/345 Log: Use result manager Modified: trunk/scripts/SiMatrix.java trunk/simulators/DefaultSimulator.java Modified: trunk/scripts/SiMatrix.java =================================================================== --- trunk/scripts/SiMatrix.java 2014-10-08 10:20:56 UTC (rev 344) +++ trunk/scripts/SiMatrix.java 2014-10-08 11:00:58 UTC (rev 345) @@ -55,10 +55,10 @@ import fr.ifremer.isisfish.entities.StrategyMonthInfo; import fr.ifremer.isisfish.entities.Zone; import fr.ifremer.isisfish.entities.ZoneDAO; +import fr.ifremer.isisfish.simulator.ResultManager; import fr.ifremer.isisfish.simulator.SimulationContext; +import fr.ifremer.isisfish.types.Month; import fr.ifremer.isisfish.types.TimeStep; -import fr.ifremer.isisfish.types.Month; -import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.util.Nocache; /** @@ -1891,7 +1891,7 @@ * @param pop population * @return Fishing mortality per group per year (computed in December) */ - public MatrixND fishingMortalityPerGroup(TimeStep step, Population pop, ResultStorage resManager) throws TopiaException { + public MatrixND fishingMortalityPerGroup(TimeStep step, Population pop, ResultManager resManager) throws TopiaException { double Fgroup = 0; double Cgroup = 0; double Mgroup = 0; @@ -1913,12 +1913,12 @@ for (TimeStep loopstep = new TimeStep(step.getYear() * 12); loopstep.beforeOrEquals(step); loopstep=loopstep.next()) { // On fait cette boucle pour contourner les aspects de cache qui font que les resultats ne sont pas recuperes - //s'ils ont deja ete calcules une fois (meme s'ils ont change depuis) + // s'ils ont deja ete calcules une fois (meme s'ils ont change depuis) // beforeOrEquals sert a bien prendre Decembre aussi MatrixND catchPerStrategyTemp = resManager.getMatrix(loopstep, pop, ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP); if (catchPerStrategy == null) { - catchPerStrategy = catchPerStrategyTemp.clone(); + catchPerStrategy = catchPerStrategyTemp.copy(); // On clone la matrice car si on fait les operations sur celle contenue dans le cache on la modifie et donc on recupere des resultats faux. } else { catchPerStrategy = catchPerStrategy.add(catchPerStrategyTemp); // Pour avoir la somme des captures sur les 12 mois Modified: trunk/simulators/DefaultSimulator.java =================================================================== --- trunk/simulators/DefaultSimulator.java 2014-10-08 10:20:56 UTC (rev 344) +++ trunk/simulators/DefaultSimulator.java 2014-10-08 11:00:58 UTC (rev 345) @@ -497,7 +497,7 @@ if (resManager.isEnabled(ResultName.MATRIX_FISHING_MORTALITY_PER_GROUP) || resManager.isEnabled(ResultName.MATRIX_TOTAL_FISHING_MORTALITY)) { MatrixND fishingMortalityPerGroup = siMatrix.fishingMortalityPerGroup(step, - pop, context.getSimulationStorage().getResultStorage()); + pop, context.getResultManager()); if (resManager.isEnabled(ResultName.MATRIX_FISHING_MORTALITY_PER_GROUP)) { resManager.addResult(step, pop, fishingMortalityPerGroup);

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r344 - in trunk: rules scripts sensitivityexports simulators
by bpoussin＠users.forge.codelutin.com 08 Oct '14

08 Oct '14

Author: bpoussin Date: 2014-10-08 12:20:56 +0200 (Wed, 08 Oct 2014) New Revision: 344 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/344 Log: use ResultManager when needed (replace ResultStorage) during export use tx with ResultStorage Modified: trunk/rules/GraviteVPUE1.java trunk/rules/TACpoids.java trunk/scripts/GravityModel.java trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java trunk/sensitivityexports/SensitivitySpawningBiomassY2.java trunk/simulators/DefaultSimulator.java Modified: trunk/rules/GraviteVPUE1.java =================================================================== --- trunk/rules/GraviteVPUE1.java 2014-08-21 15:53:43 UTC (rev 343) +++ trunk/rules/GraviteVPUE1.java 2014-10-08 10:20:56 UTC (rev 344) @@ -39,6 +39,7 @@ import fr.ifremer.isisfish.entities.*; import fr.ifremer.isisfish.rule.AbstractRule; import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.simulator.ResultManager; /** * GraviteVPUE1.java @@ -183,8 +184,7 @@ step); //List<Population> populations = SiMatrix.getSiMatrix(context) // .getPopulations(date); - ResultStorage resultmanager = context.getSimulationStorage() - .getResultStorage(); + ResultManager resultmanager = context.getResultManager(); ////////Initialisation des matrices qui resultent de la simulation//////////////////////////////////////////////////////////// Modified: trunk/rules/TACpoids.java =================================================================== --- trunk/rules/TACpoids.java 2014-08-21 15:53:43 UTC (rev 343) +++ trunk/rules/TACpoids.java 2014-10-08 10:20:56 UTC (rev 344) @@ -32,7 +32,6 @@ import scripts.ResultName; import scripts.RuleUtil; import scripts.SiMatrix; -import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.entities.EffortDescription; import fr.ifremer.isisfish.entities.Metier; import fr.ifremer.isisfish.entities.Population; @@ -43,6 +42,7 @@ import fr.ifremer.isisfish.rule.AbstractRule; import fr.ifremer.isisfish.simulator.MetierMonitor; import fr.ifremer.isisfish.simulator.PopulationMonitor; +import fr.ifremer.isisfish.simulator.ResultManager; import fr.ifremer.isisfish.simulator.SimulationContext; import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.types.Month; @@ -297,8 +297,7 @@ @Override public void postAction(SimulationContext context, TimeStep step, Metier metier) throws Exception { - ResultStorage resultmanager = context.getSimulationStorage() - .getResultStorage(); + ResultManager resultmanager = context.getResultManager(); log.info("[TAC] postAction for: " + metier); TargetSpecies ts = metier.getMetierSeasonInfo(step.getMonth()) .getSpeciesTargetSpecies(param_species); Modified: trunk/scripts/GravityModel.java =================================================================== --- trunk/scripts/GravityModel.java 2014-08-21 15:53:43 UTC (rev 343) +++ trunk/scripts/GravityModel.java 2014-10-08 10:20:56 UTC (rev 344) @@ -34,7 +34,6 @@ import org.nuiton.topia.TopiaContext; import org.nuiton.topia.TopiaException; -import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.datastore.StorageException; import fr.ifremer.isisfish.entities.EffortDescription; import fr.ifremer.isisfish.entities.Metier; @@ -43,6 +42,7 @@ import fr.ifremer.isisfish.entities.SetOfVessels; import fr.ifremer.isisfish.entities.Strategy; import fr.ifremer.isisfish.entities.Zone; +import fr.ifremer.isisfish.simulator.ResultManager; import fr.ifremer.isisfish.simulator.SimulationContext; import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.types.Month; @@ -67,7 +67,7 @@ protected SimulationContext context = null; protected TopiaContext db = null; protected SiMatrix siMatrix = null; - protected ResultStorage resultManager = null; + protected ResultManager resultManager = null; /** * Method used to get GravityModel used for simulation @@ -91,7 +91,7 @@ throws TopiaException, StorageException { this.context = context; this.db = context.getDB(); - this.resultManager = context.getSimulationStorage().getResultStorage(); + this.resultManager = context.getResultManager(); this.siMatrix = siMatrix; setGravityModel(context, this); } Modified: trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java 2014-08-21 15:53:43 UTC (rev 343) +++ trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java 2014-10-08 10:20:56 UTC (rev 344) @@ -80,8 +80,6 @@ map.put(group.getId(),group.getMaturityOgive()); } - tx.closeContext(); - //instantiate a reader that starts reading from the file end. ReverseFileReader reader = new ReverseFileReader(referenceFile); @@ -116,7 +114,7 @@ //Get the biomass of the last time step MatrixND matlastdate = resultStorage.getMatrix(pop, - ResultName.MATRIX_BIOMASS); + ResultName.MATRIX_BIOMASS, tx); for (MatrixIterator i = matlastdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); @@ -129,6 +127,8 @@ } } + tx.closeContext(); + out.write(Double.toString(biomass / referenceBiomass)); } Modified: trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java 2014-08-21 15:53:43 UTC (rev 343) +++ trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java 2014-10-08 10:20:56 UTC (rev 344) @@ -83,8 +83,6 @@ map.put(group.getId(),group.getMaturityOgive()); } - tx.closeContext(); - //instantiate a reader that starts reading from the file end. ReverseFileReader reader = new ReverseFileReader(referenceFile); @@ -124,7 +122,7 @@ //Get the biomass of the first time step MatrixND matfirstdate = resultStorage.getMatrix(pop, - ResultName.MATRIX_BIOMASS); + ResultName.MATRIX_BIOMASS, tx); for (MatrixIterator i = matfirstdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); @@ -138,7 +136,7 @@ //Get the biomass of the last time step MatrixND matlastdate = resultStorage.getMatrix(pop, - ResultName.MATRIX_BIOMASS); + ResultName.MATRIX_BIOMASS, tx); for (MatrixIterator i = matlastdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); @@ -152,6 +150,8 @@ } } + tx.closeContext(); + out.write(Double.toString((biomass / firstbiomass) / (biomassReference / firstBiomassReference))); } Modified: trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java 2014-08-21 15:53:43 UTC (rev 343) +++ trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java 2014-10-08 10:20:56 UTC (rev 344) @@ -36,6 +36,7 @@ import scripts.ResultName; import java.io.Writer; +import org.nuiton.topia.TopiaContext; public class SensitivitySpawningBiomassRelativeY5 implements SensitivityExport { @@ -58,13 +59,15 @@ double biomass = 0.0; double firstbiomass = 0.0; + ResultStorage resultStorage = simulation.getResultStorage(); + TopiaContext tx = simulation.getStorage().beginTransaction(); + for (Population pop : simulation.getParameter().getPopulations()) { if (pop.getName().equals(param_pop.getName())) { - ResultStorage resultStorage = simulation.getResultStorage(); //Get the biomass of the first time step MatrixND matfirstdate = resultStorage.getMatrix(pop, - ResultName.MATRIX_BIOMASS); + ResultName.MATRIX_BIOMASS, tx); for (MatrixIterator i = matfirstdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); @@ -78,7 +81,7 @@ //Get the biomass of the last time step MatrixND matlastdate = resultStorage.getMatrix(pop, - ResultName.MATRIX_BIOMASS); + ResultName.MATRIX_BIOMASS, tx); for (MatrixIterator i = matlastdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); @@ -89,6 +92,9 @@ } } } + + tx.closeContext(); + out.write(Double.toString(biomass / firstbiomass)); } Modified: trunk/sensitivityexports/SensitivitySpawningBiomassY2.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassY2.java 2014-08-21 15:53:43 UTC (rev 343) +++ trunk/sensitivityexports/SensitivitySpawningBiomassY2.java 2014-10-08 10:20:56 UTC (rev 344) @@ -36,6 +36,7 @@ import scripts.ResultName; import java.io.Writer; +import org.nuiton.topia.TopiaContext; public class SensitivitySpawningBiomassY2 implements SensitivityExport { @@ -56,13 +57,15 @@ TimeStep lastStep = simulation.getResultStorage().getLastStep(); double biomass = 0.0; + ResultStorage resultStorage = simulation.getResultStorage(); + TopiaContext tx = simulation.getStorage().beginTransaction(); + for (Population pop : simulation.getParameter().getPopulations()) { if (pop.getName().equals(param_pop.getName())) { - ResultStorage resultStorage = simulation.getResultStorage(); //Get the biomass of the last time step MatrixND matlastdate = resultStorage.getMatrix(pop, - ResultName.MATRIX_BIOMASS); + ResultName.MATRIX_BIOMASS, tx); for (MatrixIterator i = matlastdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); @@ -74,6 +77,9 @@ } } } + + tx.closeContext(); + out.write(Double.toString(biomass)); } Modified: trunk/simulators/DefaultSimulator.java =================================================================== --- trunk/simulators/DefaultSimulator.java 2014-08-21 15:53:43 UTC (rev 343) +++ trunk/simulators/DefaultSimulator.java 2014-10-08 10:20:56 UTC (rev 344) @@ -22,7 +22,6 @@ package simulators; import fr.ifremer.isisfish.IsisFishException; -import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.entities.Metier; import fr.ifremer.isisfish.entities.Population; import fr.ifremer.isisfish.entities.PopulationSeasonInfo; @@ -348,8 +347,7 @@ protected void computeMonth(SimulationContext context, SiMatrix siMatrix, TimeStep step, Population pop) throws IsisFishException, TopiaException { // to add result - ResultStorage resManager = context.getSimulationStorage() - .getResultStorage(); + ResultManager resManager = context.getResultManager(); PopulationMonitor popMon = context.getPopulationMonitor(); MatrixND N = popMon.getN(pop);

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