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r4303 - trunk/src/main/java/fr/ifremer/isisfish/types
by echatellier＠users.forge.codelutin.com 15 Oct '15

15 Oct '15

Author: echatellier Date: 2015-10-15 10:05:06 +0200 (Thu, 15 Oct 2015) New Revision: 4303 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4303 Log: Fix mistake Modified: trunk/src/main/java/fr/ifremer/isisfish/types/RecruitmentInput.java Modified: trunk/src/main/java/fr/ifremer/isisfish/types/RecruitmentInput.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/types/RecruitmentInput.java 2015-10-14 09:44:55 UTC (rev 4302) +++ trunk/src/main/java/fr/ifremer/isisfish/types/RecruitmentInput.java 2015-10-15 08:05:06 UTC (rev 4303) @@ -43,7 +43,7 @@ /** * RecuitementContribution (can be {@code null} if outside recruitement period). */ - protected Double recuitementContribution; + protected Double recruitementContribution; public RecruitmentInput() { super(null, null, null); @@ -61,16 +61,16 @@ * * @return recuitementContribution (can be {@code null} if outside recruitement period). */ - public Double getRecuitementContribution() { - return recuitementContribution; + public Double getRecruitementContribution() { + return recruitementContribution; } /** - * Set RecuitementContribution + * Set RecruitementContribution * - * @param recuitementContribution recuitementContribution (can be {@code null} if outside recruitement period). + * @param recruitementContribution recuitementContribution (can be {@code null} if outside recruitement period). */ - public void setRecuitementContribution(Double recuitementContribution) { - this.recuitementContribution = recuitementContribution; + public void setRecruitementContribution(Double recruitementContribution) { + this.recruitementContribution = recruitementContribution; } }

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r4302 - trunk
by echatellier＠users.forge.codelutin.com 14 Oct '15

14 Oct '15

Author: echatellier Date: 2015-10-14 11:44:55 +0200 (Wed, 14 Oct 2015) New Revision: 4302 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4302 Log: Update libs Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2015-09-29 16:46:43 UTC (rev 4301) +++ trunk/pom.xml 2015-10-14 09:44:55 UTC (rev 4302) @@ -150,7 +150,7 @@ <dependency> <groupId>javax.activation</groupId> <artifactId>activation</artifactId> - <version>1.1</version> + <version>1.1.1</version> <scope>compile</scope> </dependency> @@ -232,12 +232,6 @@ <groupId>org.apache.commons</groupId> <artifactId>commons-email</artifactId> <version>1.4</version> - <exclusions> - <exclusion> - <artifactId>activation</artifactId> - <groupId>javax.activation</groupId> - </exclusion> - </exclusions> </dependency> <dependency> @@ -256,7 +250,7 @@ <dependency> <groupId>org.apache.logging.log4j</groupId> <artifactId>log4j-core</artifactId> - <version>2.4</version> + <version>2.4.1</version> <scope>compile</scope> </dependency> @@ -263,7 +257,7 @@ <dependency> <groupId>org.apache.logging.log4j</groupId> <artifactId>log4j-api</artifactId> - <version>2.4</version> + <version>2.4.1</version> <scope>compile</scope> </dependency> @@ -270,7 +264,7 @@ <dependency> <groupId>org.apache.logging.log4j</groupId> <artifactId>log4j-jcl</artifactId> - <version>2.4</version> + <version>2.4.1</version> <scope>runtime</scope> </dependency> @@ -277,7 +271,7 @@ <dependency> <groupId>org.apache.logging.log4j</groupId> <artifactId>log4j-slf4j-impl</artifactId> - <version>2.4</version> + <version>2.4.1</version> <scope>runtime</scope> </dependency> @@ -369,7 +363,7 @@ <dependency> <groupId>org.tmatesoft.svnkit</groupId> <artifactId>svnkit</artifactId> - <version>1.8.10</version> + <version>1.8.11</version> <scope>compile</scope> <exclusions> <exclusion> @@ -418,15 +412,21 @@ <dependency> <groupId>org.assertj</groupId> <artifactId>assertj-swing</artifactId> - <version>2.1.1</version> + <version>3.0.0</version> <scope>test</scope> </dependency> <dependency> <groupId>org.assertj</groupId> <artifactId>assertj-swing-junit</artifactId> - <version>2.1.1</version> + <version>3.0.0</version> <scope>test</scope> </dependency> + <dependency> + <groupId>org.easytesting</groupId> + <artifactId>fest-reflect</artifactId> + <version>1.4.1</version> + <scope>test</scope> + </dependency> </dependencies>

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r4301 - in trunk: . src/test/java/fr/ifremer/isisfish/logging src/test/java/fr/ifremer/isisfish/mexico src/test/java/fr/ifremer/isisfish/simulator/sensitivity/domain
by echatellier＠users.forge.codelutin.com 29 Sep '15

29 Sep '15

Author: echatellier Date: 2015-09-29 18:46:43 +0200 (Tue, 29 Sep 2015) New Revision: 4301 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4301 Log: Fix broken javadoc Modified: trunk/pom.xml trunk/src/test/java/fr/ifremer/isisfish/logging/LoggerHelper.java trunk/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java trunk/src/test/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomainTest.java Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2015-09-29 15:25:33 UTC (rev 4300) +++ trunk/pom.xml 2015-09-29 16:46:43 UTC (rev 4301) @@ -576,6 +576,8 @@ <releaseEmailDomain>forge.codelutin.com</releaseEmailDomain> <releaseEmail>noreply(a)forge.codelutin.com</releaseEmail> +  + <javadocPluginVersion>2.10.3</javadocPluginVersion> <!-- jnlp (disabled until retested) <keystorepath>${codelutin.keystorepath}</keystorepath> <keystorealias>CodeLutin</keystorealias> Modified: trunk/src/test/java/fr/ifremer/isisfish/logging/LoggerHelper.java =================================================================== --- trunk/src/test/java/fr/ifremer/isisfish/logging/LoggerHelper.java 2015-09-29 15:25:33 UTC (rev 4300) +++ trunk/src/test/java/fr/ifremer/isisfish/logging/LoggerHelper.java 2015-09-29 16:46:43 UTC (rev 4301) @@ -238,20 +238,20 @@ /** * This is a log record (says an entry of a log file). This is abstracted from any * logging implementation. - * + * * To deal with log, we don't use string version stored in original log file, * prefer use serialized form of a LogRecord : we keep a lot of time when using * them to display them in ui, and for filtering process too. - * + * * The LogRecord unicity is base on two properties : * <ul> * <li>timestamp</li> * <li>message</li> * </ul> - * + * * We can not use only timestamp, more than one event could appear in a same * timestamp. - * + * * TODO Put this code in lutinLog ? * * @author chemit @@ -282,7 +282,7 @@ /** * the string represention of logEvent, transient since we use a lazy getter * we don't need to store it. - * + * * (if not transient : double the size of serialized form...) */ protected transient String text; @@ -289,7 +289,7 @@ /** * the offset of logRecord in stream. - * + * * This is a transient property, since we compute this value when getting * the LogRecord from stream */ Modified: trunk/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java =================================================================== --- trunk/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java 2015-09-29 15:25:33 UTC (rev 4300) +++ trunk/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java 2015-09-29 16:46:43 UTC (rev 4301) @@ -443,9 +443,7 @@ * @throws IsisFishException * @throws TopiaException * - * This test may fail because of testPercentageMinMaxFactor(fr.ifremer.isisfish.mexico.MexicoHelperTest) Time elapsed: 0.528 sec <<< FAILURE! - * org.junit.ComparisonFailure: expected:<...="Tue Jun 10 18:54:3[5] CEST 2014" id=""> - * ...> but was:<...="Tue Jun 10 18:54:3[6] CEST 2014" id=""> + * This test may fail because of date delay by one seconds due to slow testing */ //@Test public void testPercentageMinMaxFactor() throws IOException, IsisFishException, TopiaException { Modified: trunk/src/test/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomainTest.java =================================================================== --- trunk/src/test/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomainTest.java 2015-09-29 15:25:33 UTC (rev 4300) +++ trunk/src/test/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomainTest.java 2015-09-29 16:46:43 UTC (rev 4301) @@ -50,7 +50,7 @@ /** * Test jdistlib pour verifier que les parametres sont bien compris en compte. * - * Ici : valeurs négatives non gérées correctement (min > max). + * Ici : valeurs négatives non gérées correctement (min > max). */ @Test public void testJDistLib2() {

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r4300 - in trunk/src/main: java/fr/ifremer/isisfish/entities java/fr/ifremer/isisfish/equation java/fr/ifremer/isisfish/simulator java/fr/ifremer/isisfish/types xmi
by echatellier＠users.forge.codelutin.com 29 Sep '15

29 Sep '15

Author: echatellier Date: 2015-09-29 17:25:33 +0200 (Tue, 29 Sep 2015) New Revision: 4300 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4300 Log: ref #6194 : refactoring using recruitmentInput map Added: trunk/src/main/java/fr/ifremer/isisfish/types/RecruitmentInput.java trunk/src/main/java/fr/ifremer/isisfish/types/RecruitmentInputMap.java Removed: trunk/src/main/java/fr/ifremer/isisfish/types/ReproductionDataMap.java Modified: trunk/src/main/java/fr/ifremer/isisfish/entities/PopulationImpl.java trunk/src/main/java/fr/ifremer/isisfish/equation/PopulationRecruitmentEquation.java trunk/src/main/java/fr/ifremer/isisfish/simulator/PopulationMonitor.java trunk/src/main/xmi/isis-fish.zargo Modified: trunk/src/main/java/fr/ifremer/isisfish/entities/PopulationImpl.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/entities/PopulationImpl.java 2015-09-29 15:23:33 UTC (rev 4299) +++ trunk/src/main/java/fr/ifremer/isisfish/entities/PopulationImpl.java 2015-09-29 15:25:33 UTC (rev 4300) @@ -53,8 +53,8 @@ import fr.ifremer.isisfish.equation.PopulationRecruitmentEquation; import fr.ifremer.isisfish.equation.PopulationReproductionEquation; import fr.ifremer.isisfish.equation.PopulationReproductionRateEquation; -import fr.ifremer.isisfish.types.ReproductionDataMap; import fr.ifremer.isisfish.types.Month; +import fr.ifremer.isisfish.types.RecruitmentInputMap; import fr.ifremer.isisfish.types.TimeStep; /** @@ -764,7 +764,7 @@ } @Override - public MatrixND getRecruitmentMatrix(TimeStep step, Population pop, ReproductionDataMap abundanceAndRepros, + public MatrixND getRecruitmentMatrix(TimeStep step, Population pop, RecruitmentInputMap recruitmentInputs, MatrixND result) { try { @@ -772,7 +772,7 @@ Equation e = pop.getRecruitmentEquation(); // l'equation doit mettre les resultats dans la matrice result - e.evaluate("step", step, "pop", pop, "aboundanceAndRepros", abundanceAndRepros, + e.evaluate("step", step, "pop", pop, "recruitmentInputs", recruitmentInputs, "result", result); } catch (Exception eee) { Modified: trunk/src/main/java/fr/ifremer/isisfish/equation/PopulationRecruitmentEquation.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/equation/PopulationRecruitmentEquation.java 2015-09-29 15:23:33 UTC (rev 4299) +++ trunk/src/main/java/fr/ifremer/isisfish/equation/PopulationRecruitmentEquation.java 2015-09-29 15:25:33 UTC (rev 4300) @@ -29,7 +29,7 @@ import fr.ifremer.isisfish.entities.Population; import fr.ifremer.isisfish.simulator.SimulationContext; -import fr.ifremer.isisfish.types.ReproductionDataMap; +import fr.ifremer.isisfish.types.RecruitmentInputMap; import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.ArgTypes; import fr.ifremer.isisfish.util.Args; @@ -48,20 +48,20 @@ * @param context simulation context * @param step current time step * @param pop population pour lequel on souhaite la matrice de recrutement - * @param reproductions les abundances, biomasses et reproduction correspondant au recrutement courant + * @param recruitmentInputs les abundances, biomasses et reproduction correspondant au recrutement courant * @param result la matrice resultat que l'equation doit remplir, il s'agit * d'une matrice groupes/zones * @return la valeur retournée n'est pas utilisée, par exemple 'return 0;' convient. * @throws Exception */ - @Args({"context", "step", "pop", "reproductions", "result"}) + @Args({"context", "step", "pop", "recruitmentInputs", "result"}) @ArgTypes({ "fr.ifremer.isisfish.simulator.SimulationContext", "fr.ifremer.isisfish.types.TimeStep", "fr.ifremer.isisfish.entities.Population", - "fr.ifremer.isisfish.types.ReproductionDataMap", + "fr.ifremer.isisfish.types.RecruitmentInputMap", "org.nuiton.math.matrix.MatrixND"}) public double compute(SimulationContext context, TimeStep step, - Population pop, ReproductionDataMap reproductions, MatrixND result) throws Exception; + Population pop, RecruitmentInputMap recruitmentInputs, MatrixND result) throws Exception; } Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/PopulationMonitor.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/PopulationMonitor.java 2015-09-29 15:23:33 UTC (rev 4299) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/PopulationMonitor.java 2015-09-29 15:25:33 UTC (rev 4300) @@ -25,9 +25,9 @@ package fr.ifremer.isisfish.simulator; -import fr.ifremer.isisfish.IsisFishRuntimeException; - +import java.util.AbstractMap; import java.util.ArrayList; +import java.util.Collections; import java.util.HashMap; import java.util.List; import java.util.Map; @@ -38,19 +38,18 @@ import org.nuiton.math.matrix.MatrixIterator; import org.nuiton.math.matrix.MatrixND; +import fr.ifremer.isisfish.IsisFishRuntimeException; import fr.ifremer.isisfish.entities.Population; import fr.ifremer.isisfish.entities.PopulationGroup; import fr.ifremer.isisfish.entities.PopulationSeasonInfo; import fr.ifremer.isisfish.entities.Species; import fr.ifremer.isisfish.entities.Zone; +import fr.ifremer.isisfish.types.Month; +import fr.ifremer.isisfish.types.RecruitmentInput; +import fr.ifremer.isisfish.types.RecruitmentInputMap; import fr.ifremer.isisfish.types.ReproductionData; -import fr.ifremer.isisfish.types.ReproductionDataMap; import fr.ifremer.isisfish.types.TimeStep; -import fr.ifremer.isisfish.types.Month; -import java.util.AbstractMap; -import java.util.Collections; - /** * Classe permettant le suivi des populations de la simulation. * @@ -183,10 +182,21 @@ * @return the reproduction */ public MatrixND getReproduction(TimeStep step, Population pop) { - return this.reproductions.get(pop).get(step).getRepro(); + return getReproductionData(step, pop).getRepro(); } /** + * Return reproduction data. + * + * @param step step + * @param pop population + * @return the reproductionData + */ + public ReproductionData getReproductionData(TimeStep step, Population pop) { + return this.reproductions.get(pop).get(step); + } + + /** * Set new reproduction. * * @param step step @@ -234,8 +244,8 @@ * Une autre facon de faire est de supprimer les repro == 0 car normalement * toute la repro doit etre utilisé au bout d'un certain temps * - * @param step - * @param pop + * @param step step + * @param pop population * @return population recruitment */ public MatrixND getRecruitment(TimeStep step, Population pop) { @@ -247,7 +257,8 @@ new List[] { pop.getPopulationGroup(), pop.getPopulationZone() }); - ReproductionDataMap reproductionDataMap = new ReproductionDataMap(); + RecruitmentInputMap recruitmentInputMap = null; + PopulationSeasonInfo foundReproductionSeasonInfo = null; // pour chaque for (int e = 0; e < etalement; e++) { @@ -254,12 +265,60 @@ // recuperation de la reproduction stucture en zone repro TimeStep t = new TimeStep(step.getStep() - e - pop.getMonthGapBetweenReproRecrutement()); - + ReproductionData reproductionData = reproductions.get(pop).get(t); + // si une repro existe pour le mois + if (reproductionData != null) { - if (reproductionData != null) { // si une repro existe pour le mois - - reproductionDataMap.put(t, reproductionData); + // on ne doit fournir des datas que si une saison de reproduction existe + // en fonction du gap et de l'etalement + Month reproMonth = t.getMonth(); + PopulationSeasonInfo reproductionSeasonInfo = pop.getPopulationSeasonInfo(reproMonth); + if (reproductionSeasonInfo != null && reproductionSeasonInfo.isReproduction() && foundReproductionSeasonInfo == null) { + foundReproductionSeasonInfo = reproductionSeasonInfo; + + int monthCount = foundReproductionSeasonInfo.getMonths().size(); + recruitmentInputMap = new RecruitmentInputMap(monthCount); + int pos = reproductionSeasonInfo.getMonths().indexOf(reproMonth); + + // on remplit toutes les données relativement à la position où la reproduction a été trouvée + // exemple: si on trouve la reproduction directement sur le mois m = 2 + // on remplit la données (0) avec t + 2 + // on remplit la données (1) avec t + 1 + // on remplit la données (2) avec t + // exemple 2: si m = 1 + // on remplit la données (0) avec t + 1 + // on remplit la données (1) avec t + // on remplit la données (2) avec t - 1 + // exemple 3: si m = 0 (directement sur le premier mois) + // on remplit la données (0) avec t + // on remplit la données (1) avec t - 1 + // on remplit la données (2) avec t - 2 + for (int p = 0; p < monthCount; p++) { + TimeStep t2 = new TimeStep(t.getStep() - p + pos); + ReproductionData reproductionData2 = reproductions.get(pop).get(t2); + RecruitmentInput recruitmentInput2 = reproductionData2 != null ? new RecruitmentInput(reproductionData2) : new RecruitmentInput(); + // recruitmentInput2#recuitementContribution must be null + // this is the key "null information here" + // on remplit les case passées (-) + recruitmentInputMap.put(p, recruitmentInput2); + } + } + + // pour les mois suivants (la map est forcement remplie on ajuste seulement la contribution) + if (foundReproductionSeasonInfo != null) { + int pos = foundReproductionSeasonInfo.getMonths().indexOf(reproMonth); + + if (pos != -1) { + // si pos == -1 c'est que l'etalement + gap est au dela de la période de repro + // mais comme on a trouvé une periode de repro avant, on donne quand même + // les données avec recuitementContribution à nul + RecruitmentInput recruitmentInput = recruitmentInputMap.get(pos); + Double contribution = matEtalement.getValue(e); + recruitmentInput.setRecuitementContribution(contribution); + } + } + MatrixND repro = reproductionData.getRepro(); // on fait la correspondance entre les zones repro et @@ -335,7 +394,9 @@ } // calcul recrutement par l'equation - result = pop.getRecruitmentMatrix(step, pop, reproductionDataMap, result); + if (recruitmentInputMap != null) { + result = pop.getRecruitmentMatrix(step, pop, recruitmentInputMap, result); + } return result; } @@ -342,7 +403,7 @@ /** * @param pop population - * @param catchPerStrategyMet + * @param catchPerStrategyMet */ public void holdCatch(Population pop, MatrixND catchPerStrategyMet) { catchs.put(pop, catchPerStrategyMet); Added: trunk/src/main/java/fr/ifremer/isisfish/types/RecruitmentInput.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/types/RecruitmentInput.java (rev 0) +++ trunk/src/main/java/fr/ifremer/isisfish/types/RecruitmentInput.java 2015-09-29 15:25:33 UTC (rev 4300) @@ -0,0 +1,76 @@ +/* + * #%L + * IsisFish + * + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2015 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 + * 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.types; + +/** + * Data used to compute recruitement equation. + * + * Contains: + * <ul> + * <li>Aboundance (for related month)</li> + * <li>Biomass (for related month)</li> + * <li>Repro (for related month)</li> + * <li>recuitementContribution (can be null if outside recruitemnent period)</li> + * </ul> + * + * @author Eric Chatellier + * @since 4.4.0.0 + */ +public class RecruitmentInput extends ReproductionData { + + /** + * RecuitementContribution (can be {@code null} if outside recruitement period). + */ + protected Double recuitementContribution; + + public RecruitmentInput() { + super(null, null, null); + } + + public RecruitmentInput(ReproductionData data) { + super(data.getAboundance(), + data.getBiomass(), + data.getRepro()); + + } + + /** + * RecuitementContribution + * + * @return recuitementContribution (can be {@code null} if outside recruitement period). + */ + public Double getRecuitementContribution() { + return recuitementContribution; + } + + /** + * Set RecuitementContribution + * + * @param recuitementContribution recuitementContribution (can be {@code null} if outside recruitement period). + */ + public void setRecuitementContribution(Double recuitementContribution) { + this.recuitementContribution = recuitementContribution; + } +} Property changes on: trunk/src/main/java/fr/ifremer/isisfish/types/RecruitmentInput.java ___________________________________________________________________ Added: svn:keywords ## -0,0 +1 ## +Author Date Id Revision HeadURL \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: trunk/src/main/java/fr/ifremer/isisfish/types/RecruitmentInputMap.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/types/RecruitmentInputMap.java (rev 0) +++ trunk/src/main/java/fr/ifremer/isisfish/types/RecruitmentInputMap.java 2015-09-29 15:25:33 UTC (rev 4300) @@ -0,0 +1,46 @@ +/* + * #%L + * IsisFish + * + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2015 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 + * 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.types; + +import java.util.HashMap; + +/** + * Map instance to use a simplier object in model. + * + * @since 4.4.0.0 + */ +public class RecruitmentInputMap extends HashMap<Integer, RecruitmentInput> { + + /** serialVersionUID. */ + private static final long serialVersionUID = 2765995771062359295L; + + public RecruitmentInputMap() { + super(); + } + + public RecruitmentInputMap(int initialCapacity) { + super(initialCapacity); + } +} Property changes on: trunk/src/main/java/fr/ifremer/isisfish/types/RecruitmentInputMap.java ___________________________________________________________________ Added: svn:keywords ## -0,0 +1 ## +Author Date Id Revision HeadURL \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Deleted: trunk/src/main/java/fr/ifremer/isisfish/types/ReproductionDataMap.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/types/ReproductionDataMap.java 2015-09-29 15:23:33 UTC (rev 4299) +++ trunk/src/main/java/fr/ifremer/isisfish/types/ReproductionDataMap.java 2015-09-29 15:25:33 UTC (rev 4300) @@ -1,39 +0,0 @@ -/* - * #%L - * IsisFish - * - * $Id$ - * $HeadURL$ - * %% - * Copyright (C) 2015 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 - * 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.types; - -import java.util.HashMap; - -/** - * Map instance to use a sinplier object in model. - * - * @since 4.4.0.0 - */ -public class ReproductionDataMap extends HashMap<TimeStep, ReproductionData> { - - /** serialVersionUID. */ - private static final long serialVersionUID = 2765995771062359295L; - -} Modified: trunk/src/main/xmi/isis-fish.zargo =================================================================== (Binary files differ)

1 0

r4299 - trunk
by echatellier＠users.forge.codelutin.com 29 Sep '15

29 Sep '15

Author: echatellier Date: 2015-09-29 17:23:33 +0200 (Tue, 29 Sep 2015) New Revision: 4299 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4299 Log: Fix dependencies (again !!!) Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2015-09-28 09:12:16 UTC (rev 4298) +++ trunk/pom.xml 2015-09-29 15:23:33 UTC (rev 4299) @@ -147,6 +147,13 @@ <scope>compile</scope> </dependency> + <dependency> + <groupId>javax.activation</groupId> + <artifactId>activation</artifactId> + <version>1.1</version> + <scope>compile</scope> + </dependency> +  <dependency> <groupId>org.nuiton.jaxx</groupId>

1 0

r4298 - trunk/src/main/java/fr/ifremer/isisfish/ui/input/equation
by echatellier＠users.forge.codelutin.com 28 Sep '15

28 Sep '15

Author: echatellier Date: 2015-09-28 11:12:16 +0200 (Mon, 28 Sep 2015) New Revision: 4298 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4298 Log: set extension lower case Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/input/equation/InputOneEquationHandler.java Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/input/equation/InputOneEquationHandler.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/input/equation/InputOneEquationHandler.java 2015-09-28 08:48:01 UTC (rev 4297) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/input/equation/InputOneEquationHandler.java 2015-09-28 09:12:16 UTC (rev 4298) @@ -203,7 +203,7 @@ } protected void saveModel() { - saveAsModel(inputContentUI.formuleCategory, "Java", inputContentUI.editor.getText()); + saveAsModel(inputContentUI.formuleCategory, "java", inputContentUI.editor.getText()); setComboModel(); inputContentUI.setInfoText(t("isisfish.message.saveModel.finished")); }

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r4297 - trunk
by echatellier＠users.forge.codelutin.com 28 Sep '15

28 Sep '15

Author: echatellier Date: 2015-09-28 10:48:01 +0200 (Mon, 28 Sep 2015) New Revision: 4297 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4297 Log: Update libs and fix dependencies Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2015-07-06 14:49:01 UTC (rev 4296) +++ trunk/pom.xml 2015-09-28 08:48:01 UTC (rev 4297) @@ -65,6 +65,13 @@ <version>${hibernateVersion}</version> <scope>compile</scope> </dependency> + + <dependency> + <groupId>org.hibernate</groupId> + <artifactId>hibernate-ehcache</artifactId> + <version>${hibernateVersion}</version> + <scope>runtime</scope> + </dependency>  <dependency> @@ -112,7 +119,7 @@ <dependency> <groupId>com.fifesoft</groupId> <artifactId>rsyntaxtextarea</artifactId> - <version>2.5.7</version> + <version>2.5.8</version> </dependency> <dependency> @@ -134,16 +141,10 @@ </dependency> --> <dependency> - <groupId>javax.mail</groupId> - <artifactId>mail</artifactId> - <version>1.4.7</version> + <groupId>com.sun.mail</groupId> + <artifactId>javax.mail</artifactId> + <version>1.5.4</version> <scope>compile</scope> - <exclusions> - <exclusion> - <artifactId>activation</artifactId> - <groupId>javax.activation</groupId> - </exclusion> - </exclusions> </dependency>  @@ -248,7 +249,7 @@ <dependency> <groupId>org.apache.logging.log4j</groupId> <artifactId>log4j-core</artifactId> - <version>2.3</version> + <version>2.4</version> <scope>compile</scope> </dependency> @@ -255,7 +256,7 @@ <dependency> <groupId>org.apache.logging.log4j</groupId> <artifactId>log4j-api</artifactId> - <version>2.3</version> + <version>2.4</version> <scope>compile</scope> </dependency> @@ -262,7 +263,7 @@ <dependency> <groupId>org.apache.logging.log4j</groupId> <artifactId>log4j-jcl</artifactId> - <version>2.3</version> + <version>2.4</version> <scope>runtime</scope> </dependency> @@ -269,7 +270,7 @@ <dependency> <groupId>org.apache.logging.log4j</groupId> <artifactId>log4j-slf4j-impl</artifactId> - <version>2.3</version> + <version>2.4</version> <scope>runtime</scope> </dependency> @@ -325,7 +326,7 @@ <dependency> <groupId>org.aspectj</groupId> <artifactId>aspectjweaver</artifactId> - <version>1.8.6</version> + <version>1.8.7</version> </dependency> <dependency> @@ -345,6 +346,14 @@ <groupId>dsol</groupId> <artifactId>dsol-xml</artifactId> </exclusion> + <exclusion> + <artifactId>jfreechart</artifactId> + <groupId>jfree</groupId> + </exclusion> + <exclusion> + <artifactId>jcommon</artifactId> + <groupId>jfree</groupId> + </exclusion> </exclusions> </dependency>  @@ -375,7 +384,7 @@ <dependency> <groupId>org.freemarker</groupId> <artifactId>freemarker</artifactId> - <version>2.3.22</version> + <version>2.3.23</version> <scope>compile</scope> </dependency> @@ -402,13 +411,13 @@ <dependency> <groupId>org.assertj</groupId> <artifactId>assertj-swing</artifactId> - <version>2.1.0</version> + <version>2.1.1</version> <scope>test</scope> </dependency> <dependency> <groupId>org.assertj</groupId> <artifactId>assertj-swing-junit</artifactId> - <version>2.1.0</version> + <version>2.1.1</version> <scope>test</scope> </dependency> </dependencies> @@ -548,10 +557,10 @@ <redmine.statusIds>3,10,11,18,19</redmine.statusIds>  - <jaxxVersion>2.24</jaxxVersion> + <jaxxVersion>2.26</jaxxVersion> <eugeneVersion>2.14</eugeneVersion> - <topiaVersion>2.9.5.5</topiaVersion> - <hibernateVersion>4.3.10.Final</hibernateVersion> + <topiaVersion>2.11</topiaVersion> + <hibernateVersion>4.3.11.Final</hibernateVersion> <nuitonI18nVersion>3.3</nuitonI18nVersion> <nuitonWidgetsVersion>1.1.1</nuitonWidgetsVersion>

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r4296 - trunk
by ＠users.forge.codelutin.com 06 Jul '15

06 Jul '15

Author: Date: 2015-07-06 14:49:01 +0000 (Mon, 06 Jul 2015) New Revision: 4296 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4296 Log: Update rstaui & rsyntaxtextarea Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2015-06-26 15:33:58 UTC (rev 4295) +++ trunk/pom.xml 2015-07-06 14:49:01 UTC (rev 4296) @@ -112,25 +112,25 @@ <dependency> <groupId>com.fifesoft</groupId> <artifactId>rsyntaxtextarea</artifactId> - <version>2.5.6</version> + <version>2.5.7</version> </dependency> <dependency> <groupId>com.fifesoft</groupId> <artifactId>rstaui</artifactId> - <version>2.5.4</version> + <version>2.5.7</version> </dependency>  <dependency>

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r4295 - trunk/src/main/java/fr/ifremer/isisfish/simulator
by echatellier＠users.forge.codelutin.com 26 Jun '15

26 Jun '15

Author: echatellier Date: 2015-06-26 15:33:58 +0000 (Fri, 26 Jun 2015) New Revision: 4295 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4295 Log: Add missing exceptions log Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationExportResultWrapper.java Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationExportResultWrapper.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationExportResultWrapper.java 2015-06-24 08:20:02 UTC (rev 4294) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationExportResultWrapper.java 2015-06-26 15:33:58 UTC (rev 4295) @@ -261,12 +261,18 @@ // pour les Export e.export(simulation); } catch (Exception eee) { + if (log.isErrorEnabled()) { + log.error("Can't export results", eee); + } e.setException(eee); } try { // pour les ExportStep e.exportEnd(simulation); } catch (Exception eee) { + if (log.isErrorEnabled()) { + log.error("Can't export results", eee); + } e.setException(eee); } // il n'y aura plus d'ecriture dans le fichier on le ferme

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[ANN] - ISIS-Fish 4.4.0.0-rc-3 released
by codelutin.com Release Notification 24 Jun '15

24 Jun '15

The ISIS-Fish team is pleased to announce the isis-fish-4.4.0.0-rc-3 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: New features: o Détecter la non présence de "package" dans un script Issue: 7149. Thanks to Eric Chatellier. Resolved by echatellier. o changement reproduction/recrutement Issue: 6194. Thanks to stephanie MAHEVAS. Resolved by echatellier. o Ajouter une option pour supprimer les resultats en fin de simulation (après les exports). Issue: 7223. Thanks to Eric Chatellier. Resolved by echatellier. o Ajouter des champs dans la region pour changer la methode de calcul de F Issue: 7224. Thanks to Eric Chatellier. Resolved by echatellier. o Add result storage to manage resultat as script files Issue: 7210. Thanks to Eric Chatellier. Resolved by echatellier. o Détecter les metiers qui ne couvre pas toutes les saisons Issue: 5191. Thanks to Eric Chatellier. Resolved by echatellier. o Compress export file Issue: 6320. Thanks to Benjamin Poussin. Resolved by bpoussin. o Add Historic object on SimulationPlan and Optimization to store some value (parameter, objective, ...) Issue: 6321. Thanks to Benjamin Poussin. Resolved by bpoussin. o Améliorer l'affichage des informations d'une simulation Issue: 6341. Thanks to Benjamin Poussin. Resolved by bpoussin. o Matrix returned by ResultManager must be not modifiable Issue: 1728. Thanks to Benjamin Poussin. Resolved by bpoussin. o export de resultats durant la simulation Issue: 5844. Thanks to Sigrid Lehuta. Resolved by bpoussin. o Add new method on ResultManager to get matrix for multiple step Issue: 1729. Thanks to Benjamin Poussin. Resolved by bpoussin. o Passer le niveau de log des valeurs négative en warn Issue: 5936. Thanks to Eric Chatellier. Resolved by echatellier. o Change DefaultSimulator, SiMatrix and GravityModel to permit easy overwrite method to create new simulator Issue: 6322. Thanks to Benjamin Poussin. Resolved by bpoussin. Fixed Bugs: o Pouvoir réordonner les regles Issue: 7172. Thanks to Eric Chatellier. Resolved by echatellier. o Ajouter le calcul de landing weight Issue: 7222. Thanks to Eric Chatellier. Resolved by echatellier. o interface population en anglais Issue: 7019. Thanks to Sigrid Lehuta. Resolved by echatellier. o Cannot restore sensitivity analysis factor on rule Issue: 7230. Thanks to Eric Chatellier. Resolved by echatellier. o Erreur après sauvegarde d'une base Issue: 5861. Thanks to Sigrid Lehuta. Resolved by echatellier. o simule decembre 1 alors qu on demande 20 mois de simu Issue: 6311. Thanks to Sigrid Lehuta. Resolved by echatellier. o Matrix decorator fail to decorate semantics outside simulation Issue: 5632. Thanks to Eric Chatellier. Resolved by bpoussin. o Impossible de remplir la matrice de migration dans l'interface Issue: 5935. Thanks to Eric Chatellier. Resolved by kmorin. o IsisFish n'execute pas les simulations sous Java 8 Issue: 6259. Thanks to Eric Chatellier. Resolved by echatellier. o IsisFish ne détecte pas R 3.x sous windows Issue: 4296. Thanks to Eric Chatellier. Resolved by echatellier. o Parametrer les simulations en mois Issue: 5932. Thanks to Eric Chatellier. Resolved by kmorin. o Use R system jri library Issue: 5689. Thanks to Eric Chatellier. Resolved by echatellier. o Dépendances non incluses dans la simulation Issue: 568. Thanks to Jean Couteau. Resolved by echatellier. o pour un graphique dans l interface de resultats Issue: 5646. Thanks to Sigrid Lehuta. Resolved by echatellier. o Charger une région depuis une simulation Issue: 3884. Thanks to Sigrid Lehuta. Resolved by kmorin. o zone de selection Issue: 3885. Thanks to Sigrid Lehuta. Resolved by kmorin. o Erreur après la copie ou l'export d'une région Issue: 5491. Thanks to Eric Chatellier. Resolved by kmorin. Changes: o Extract static version to properties file Issue: 5688. 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-4.4.0.0-rc-1-bin.zip - http://forge.codelutin.com/attachments/download/3151 * isis-fish-4.4.0.0-rc-2-bin.zip - http://forge.codelutin.com/attachments/download/3272 * isis-fish-4.4.0.0-rc-3-bin.zip - http://forge.codelutin.com/attachments/download/3290 Maven artifacts --------------- Artifacts are deployed in nuiton maven repository http://maven.nuiton.org/other-releases/ Have fun! -ISIS-Fish team

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