August 2012 - Isis-fish-commits - mailman.cloud.codelutin.com

r3754 - trunk/src/main/java/fr/ifremer/isisfish/datastore
by bpoussin＠users.forge.codelutin.com 31 Aug '12

31 Aug '12

Author: bpoussin Date: 2012-08-31 20:17:43 +0200 (Fri, 31 Aug 2012) New Revision: 3754 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3754 Log: avec un peu de cache, ca va beaucoup mieux :) 13min -> 50s y'a plus qu'a verifier reellement les resultats :) Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java 2012-08-31 16:16:11 UTC (rev 3753) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java 2012-08-31 18:17:43 UTC (rev 3754) @@ -27,6 +27,7 @@ import fr.ifremer.isisfish.IsisFishDAOHelper; import fr.ifremer.isisfish.IsisFishException; +import fr.ifremer.isisfish.IsisFishRuntimeException; import fr.ifremer.isisfish.entities.ActiveRule; import fr.ifremer.isisfish.entities.ActiveRuleDAO; import fr.ifremer.isisfish.entities.Population; @@ -47,11 +48,14 @@ import java.util.Arrays; import java.util.Collection; import java.util.Collections; +import java.util.HashMap; import java.util.HashSet; import java.util.List; import java.util.Map; import java.util.Set; import java.util.TreeMap; +import org.apache.commons.collections.BidiMap; +import org.apache.commons.collections.bidimap.DualHashBidiMap; import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; @@ -109,6 +113,8 @@ static final private String SEP = ":"; protected TopiaContext tx; + /** en cle les representation interne (get) en valeur les valeurs decoree (getKey) */ + protected BidiMap cache = new DualHashBidiMap(); public EntitySemanticsDecorator() { } @@ -118,47 +124,54 @@ } public Object decorate(Object internalValue) { - Object result = internalValue; - if (internalValue instanceof String) { - if (StringUtils.startsWith((String)internalValue, Month.class.getName())) { - String val = StringUtils.substringAfter((String)internalValue, SEP); - int monthNumber = Integer.parseInt(val); - result = new Month(monthNumber); - } else if (StringUtils.startsWith((String)internalValue, TimeStep.class.getName())) { - String val = StringUtils.substringAfter((String)internalValue, SEP); - int stepNumber = Integer.parseInt(val); - result = new TimeStep(stepNumber); - } else if (StringUtils.startsWith((String)internalValue, "fr.ifremer.isisfish.entities.")) { - if (tx == null) { - result = StringUtils.substringAfter((String)internalValue, SEP); - } else { - try { - String id = StringUtils.substringBefore((String)internalValue, SEP); - result = tx.findByTopiaId(id); - } catch (TopiaException eee) { - log.info("Fallback use string representation because" - + " i can't decorate (String->Entity): " - + internalValue, eee); - // si on arrive pas a convertir cette fois-ci, on - // renvoi internalValue pour que le undecorate est toutes les infos - // et donc que la prochaine fois on y arrive peut etre + Object result = cache.get(internalValue); + if (result == null && internalValue != null) { + result = internalValue; + if (internalValue instanceof String) { + if (StringUtils.startsWith((String)internalValue, Month.class.getName())) { + String val = StringUtils.substringAfter((String)internalValue, SEP); + int monthNumber = Integer.parseInt(val); + result = new Month(monthNumber); + } else if (StringUtils.startsWith((String)internalValue, TimeStep.class.getName())) { + String val = StringUtils.substringAfter((String)internalValue, SEP); + int stepNumber = Integer.parseInt(val); + result = new TimeStep(stepNumber); + } else if (StringUtils.startsWith((String)internalValue, "fr.ifremer.isisfish.entities.")) { + if (tx == null) { + result = StringUtils.substringAfter((String)internalValue, SEP); + } else { + try { + String id = StringUtils.substringBefore((String)internalValue, SEP); + result = tx.findByTopiaId(id); + } catch (TopiaException eee) { + log.info("Fallback use string representation because" + + " i can't decorate (String->Entity): " + + internalValue, eee); + // si on arrive pas a convertir cette fois-ci, on + // renvoi internalValue pour que le undecorate est toutes les infos + // et donc que la prochaine fois on y arrive peut etre + } } } } + cache.put(internalValue, result); } return result; } public Object undecorate(Object decoratedValue) { - String result; - if (decoratedValue instanceof Month) { - result = Month.class.getName() + SEP + ((Month)decoratedValue).getMonthNumber(); - } else if (decoratedValue instanceof TimeStep) { - result = TimeStep.class.getName() + SEP + ((TimeStep)decoratedValue).getStep(); - } else if (decoratedValue instanceof TopiaEntity) { - result = ((TopiaEntity)decoratedValue).getTopiaId() + SEP + decoratedValue; - } else { - result = String.valueOf(decoratedValue); + Object result = cache.getKey(decoratedValue); + if (result == null && decoratedValue != null) { + if (decoratedValue instanceof Month) { + result = Month.class.getName() + SEP + ((Month)decoratedValue).getMonthNumber(); + } else if (decoratedValue instanceof TimeStep) { + result = TimeStep.class.getName() + SEP + ((TimeStep)decoratedValue).getStep(); + } else if (decoratedValue instanceof TopiaEntity) { + result = ((TopiaEntity)decoratedValue).getTopiaId() + SEP + decoratedValue; + } else { + result = String.valueOf(decoratedValue); + } + cache.put(result, decoratedValue); } return result; } @@ -575,6 +588,19 @@ return getMatrix(step, newName, null); } + /** + * Retourne la matrice stocke pour un pas de temps + * @param step le pas de temps que l'on souhaite + * @param pop la population pour lequelle on souhaite le resultat + * @param name le nom des resultats dont on veut la matrice + * @return La matrice demandée ou null si aucune matrice ne correspond a + * la demande. + */ + public MatrixND getMatrix(TimeStep step, Population pop, String name, TopiaContext tx) { + String newName = name + " " + pop; + return getMatrix(step, newName, tx); + } + public MatrixND getMatrix(TimeStep step, String name) { return getMatrix(step, name, null); } @@ -588,6 +614,7 @@ ResultMapped r = getResult(step, name); MatrixND mat = null; if (r != null) { + tx = getTx(tx); mat = r.getMatrix(tx); } return mat; @@ -704,6 +731,7 @@ if (resultMat != null) { // on decore la matrice resultat au dernier moment, tous les calcules // ce font avec les strings + tx = getTx(tx); resultMat = new MatrixSemanticsDecorator(resultMat, new EntitySemanticsDecorator(tx)); } return resultMat; @@ -763,6 +791,29 @@ return result; } + /** + * Try to find better tx. If argument is not null, return it. otherwize + * try to get tx in SimulationContext. + * + * @param tx + * @return + */ + protected TopiaContext getTx(TopiaContext tx) { + TopiaContext result = tx; + if (tx == null) { + // si on a pas de tx, on recherche si on est dans une simulation + // pour recuperer la tx de la simulation + if (simulation == SimulationContext.get().getSimulationStorage()) { + try { + result = SimulationContext.get().getDB(); + } catch (TopiaException eee) { + throw new IsisFishRuntimeException("Can't get database from SimulationContext", eee); + } + } + } + return result; + } + /* * @see fr.ifremer.isisfish.simulator.SimulationListener#afterSimulation(fr.ifremer.isisfish.simulator.SimulationContext) */

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r3753 - trunk/src/main/java/fr/ifremer/isisfish/datastore
by bpoussin＠users.forge.codelutin.com 31 Aug '12

31 Aug '12

Author: bpoussin Date: 2012-08-31 18:16:11 +0200 (Fri, 31 Aug 2012) New Revision: 3753 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3753 Log: petit oubli du add :( Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java 2012-08-31 16:11:36 UTC (rev 3752) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java 2012-08-31 16:16:11 UTC (rev 3753) @@ -253,6 +253,7 @@ sems[i] = undecorate; for (Object o : l) { o = deco.undecorate(o); + undecorate.add(o); raf.writeUTF(o.toString()); // ecriture de chaque dimension } }

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r3752 - trunk/src/main/java/fr/ifremer/isisfish/datastore
by echatellier＠users.forge.codelutin.com 31 Aug '12

31 Aug '12

Author: echatellier Date: 2012-08-31 18:11:36 +0200 (Fri, 31 Aug 2012) New Revision: 3752 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3752 Log: Extract common interface for ResultStorage Added: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultDatabaseStorage.java Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java Copied: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultDatabaseStorage.java (from rev 3750, trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java) =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultDatabaseStorage.java (rev 0) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultDatabaseStorage.java 2012-08-31 16:11:36 UTC (rev 3752) @@ -0,0 +1,811 @@ +/* + * #%L + * IsisFish + * + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2002 - 2011 Ifremer, Code Lutin, Cédric Pineau, 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 2 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-2.0.html>. + * #L% + */ + +package fr.ifremer.isisfish.datastore; + +import static org.nuiton.i18n.I18n._; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.HashSet; +import java.util.List; +import java.util.Set; + +import org.apache.commons.collections.map.ReferenceMap; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.nuiton.math.matrix.MatrixFactory; +import org.nuiton.math.matrix.MatrixIterator; +import org.nuiton.math.matrix.MatrixND; +import org.nuiton.topia.TopiaContext; +import org.nuiton.topia.TopiaException; +import org.nuiton.util.ArrayUtil; +import org.nuiton.util.HashList; + +import fr.ifremer.isisfish.IsisFishDAOHelper; +import fr.ifremer.isisfish.IsisFishException; +import fr.ifremer.isisfish.entities.ActiveRule; +import fr.ifremer.isisfish.entities.ActiveRuleDAO; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.entities.Result; +import fr.ifremer.isisfish.entities.ResultDAO; +import fr.ifremer.isisfish.export.Export; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.rule.Rule; +import fr.ifremer.isisfish.simulator.SimulationContext; +import fr.ifremer.isisfish.simulator.SimulationException; +import fr.ifremer.isisfish.simulator.SimulationPlan; +import fr.ifremer.isisfish.simulator.SimulationResultGetter; +import fr.ifremer.isisfish.types.TimeStep; +import fr.ifremer.isisfish.types.Month; + +/** + * Cette classe permet de conserver des résultats de simulation. Elle permet + * ensuite de les récupérer. + * + * Created: 29 sept. 2004 + * + * @author Benjamin Poussin <poussin(a)codelutin.com> + * @version $Revision$ + * + * Mise a jour: $Date$ + * par : $Author$ + */ +public class ResultDatabaseStorage implements SimulationResultGetter, ResultStorage { // ResultDatabaseStorage + + /** to use log facility, just put in your code: log.info(\"...\"); */ + static private Log log = LogFactory.getLog(ResultDatabaseStorage.class); + + protected SimulationStorage simulation = null; + // transient protected HashMap<String, MatrixND> globalMatrix = new HashMap<String, MatrixND>(); + transient protected ReferenceMap cacheContext = new ReferenceMap(ReferenceMap.HARD, ReferenceMap.WEAK); + + /** cache to maintains some result. key: String(date + ':' + name), value: matrix + * TODO: cache will be more efficient if it keep at min the number of result by year */ + transient protected ReferenceMap cache = new ReferenceMap(ReferenceMap.HARD, ReferenceMap.SOFT); + /** contains all available result as string: String(date + ':' + name) */ + transient protected Set<String> availableResult = null; + /** result enabled */ + transient protected Set<String> enabledResult = null; + + /** + * Les ResultStorage ne doivent pas etre instancier directement, mais + * recuperer a partir d'un + * {@link fr.ifremer.isisfish.datastore.SimulationStorage#getResultStorage()} + * + * @param simulation storage to get result + */ + public ResultDatabaseStorage(SimulationStorage simulation) { + this.simulation = simulation; + } + + protected void putInCache(TimeStep step, String name, MatrixND mat, TopiaContext context) { + String key = step.getStep() + ":" + name; + putInCache(key, mat, context); + } + + protected void putInCache(String name, MatrixND mat, TopiaContext context) { + if (mat != null) { + cache.put(name, mat); + cacheContext.put(name, context); + } + } + + /** + * Result can be removed from cache when computed result (from multiple step) + * become invalidated by new step result. + * + * @param name result name to remove + */ + protected void removeInCache(String name) { + cache.remove(name); + cacheContext.remove(name); + } + + protected MatrixND getInCache(TimeStep step, String name) { + // do not use toString for step (depend on i18n) + String key = step.getStep() + ":" + name; + MatrixND result = getInCache(key); + return result; + } + + protected MatrixND getInCache(String name) { + MatrixND result = null; + TopiaContext context = (TopiaContext) cacheContext.get(name); + if (context != null && !context.isClosed()) { + // on verifie que le context existe encore car on peut vouloir + // naviguer dans les semantics + result = (MatrixND) cache.get(name); + } + return result; + } + + /** + * Retourne le nom de tous les resultats disponibles le nom est constitué + * de la date et du nom du resultat. + * + * @return available results + */ + protected Set<String> getAvailableResult() { + if (availableResult == null) { + availableResult = new HashSet<String>(); + try { + TopiaContext tx = null; + boolean mustClose = false; + + if (simulation == SimulationContext.get().getSimulationStorage()) { + tx = SimulationContext.get().getDbResult(); + } + + if (tx == null) { + // not in simulation, create transaction + tx = simulation.getStorage().beginTransaction(); + mustClose = true; + } + + List<String> result = (List<String>) tx.findAll("Select " + Result.PROPERTY_RESULT_STEP + "||':'||name from fr.ifremer.isisfish.entities.Result"); + if (mustClose) { + tx.closeContext(); + } + availableResult.addAll(result); + } catch (Exception eee) { + if (log.isWarnEnabled()) { + log.warn("Can't get result available", eee); + } + } + } + return availableResult; + } + + /** + * Verifie si un resultat est disponible pour une date donnée. + * + * @param step + * @param name + * @return {@code true} if result is available + */ + protected boolean isAvailableResult(TimeStep step, String name) { + String key = step.getStep() + ":" + name; + boolean result = getAvailableResult().contains(key); + return result; + } + + /** + * Ajoute un resultat comme etant disponible pour une date donnée. + * + * @param step + * @param name + */ + protected void addAvailableResult(TimeStep step, String name) { + String key = step.getStep() + ":" + name; + getAvailableResult().add(key); + } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#isEnabled(java.lang.String) + */ + @Override + public boolean isEnabled(String name) { + name = name.trim(); + if (enabledResult == null) { + enabledResult = new HashSet<String>(); + + Collection<String> resultEnabled = simulation.getParameter() + .getResultEnabled(); + enabledResult.addAll(resultEnabled); + + // test on export + List<String> exportNames = simulation.getParameter().getExportNames(); + if (exportNames != null) { + for (String exportName : exportNames) { + ExportStorage storage = ExportStorage.getExport(exportName); + try { + Export export = storage.getNewExportInstance(); + for (String resultName : export.getNecessaryResult()) { + enabledResult.add(resultName); + } + } catch (IsisFishException eee) { + if (log.isWarnEnabled()) { + log.warn(_("isisfish.error.instanciate.export", + exportName), eee); + } + } + } + } + + // test on sensitivity export + List<SensitivityExport> sensitivityExports = simulation + .getParameter().getSensitivityExport(); + if (sensitivityExports != null) { + for (SensitivityExport sensitivityExport : sensitivityExports) { + for (String resultName : sensitivityExport.getNecessaryResult()) { + enabledResult.add(resultName); + } + } + } + + // test on rules + List<Rule> rules = simulation.getParameter().getRules(); + if (rules != null) { + for (Rule rule : rules) { + for (String resultName : rule.getNecessaryResult()) { + enabledResult.add(resultName); + } + } + } + + // test on plans + List<SimulationPlan> plans = simulation.getParameter().getSimulationPlans(); + if (plans != null) { + for (SimulationPlan plan : plans) { + for (String resultName : plan.getNecessaryResult()) { + enabledResult.add(resultName); + } + } + } + log.info("Enabled result: " + enabledResult); + } + boolean result = enabledResult.contains(name); + return result; + } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#addResult(fr.ifremer.isisfish.types.TimeStep, org.nuiton.math.matrix.MatrixND) + */ + @Override + public void addResult(TimeStep step, MatrixND mat) throws IsisFishException { + addResult(false, step, mat.getName(), mat); + } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#addResult(fr.ifremer.isisfish.types.TimeStep, fr.ifremer.isisfish.entities.Population, org.nuiton.math.matrix.MatrixND) + */ + @Override + public void addResult(TimeStep step, Population pop, MatrixND mat) throws IsisFishException { + addResult(false, step, mat.getName(), pop, mat); + } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#addResult(boolean, fr.ifremer.isisfish.types.TimeStep, org.nuiton.math.matrix.MatrixND) + */ + @Override + public void addResult(boolean force, TimeStep step, MatrixND mat) throws IsisFishException { + addResult(force, step, mat.getName(), mat); + } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#addResult(boolean, fr.ifremer.isisfish.types.TimeStep, fr.ifremer.isisfish.entities.Population, org.nuiton.math.matrix.MatrixND) + */ + @Override + public void addResult(boolean force, TimeStep step, Population pop, MatrixND mat) throws IsisFishException { + addResult(force, step, mat.getName(), pop, mat); + } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#addResult(fr.ifremer.isisfish.types.TimeStep, java.lang.String, fr.ifremer.isisfish.entities.Population, org.nuiton.math.matrix.MatrixND) + */ + @Override + public void addResult(TimeStep step, String name, Population pop, MatrixND mat) throws IsisFishException { + addResult(false, step, name, pop, mat); + } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#addResult(fr.ifremer.isisfish.types.TimeStep, java.lang.String, org.nuiton.math.matrix.MatrixND) + */ + @Override + public void addResult(TimeStep step, String name, MatrixND mat) throws IsisFishException { + addResult(false, step, name, mat); + } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#addResult(boolean, fr.ifremer.isisfish.types.TimeStep, java.lang.String, fr.ifremer.isisfish.entities.Population, org.nuiton.math.matrix.MatrixND) + */ + @Override + public void addResult(boolean force, TimeStep step, String name, Population pop, MatrixND mat) throws IsisFishException { + if (force || isEnabled(name)) { + doAddResult(step, name + " " + pop, mat); + } + } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#addResult(boolean, fr.ifremer.isisfish.types.TimeStep, java.lang.String, org.nuiton.math.matrix.MatrixND) + */ + @Override + public void addResult(boolean force, TimeStep step, String name, MatrixND mat) throws IsisFishException { + if (force || isEnabled(name)) { + doAddResult(step, name, mat); + } + } + + protected void doAddResult(TimeStep step, String name, MatrixND mat) throws IsisFishException { + try { + TopiaContext tx = null; + boolean mustClose = false; + + if (simulation == SimulationContext.get().getSimulationStorage()) { + tx = SimulationContext.get().getDbResult(); + } + if (tx == null) { + // not in simulation, create transaction + tx = simulation.getStorage().beginTransaction(); + mustClose = true; + } + doAddResult(step, name, mat, tx); + if (mustClose) { + tx.commitTransaction(); + tx.closeContext(); + } + } catch (TopiaException eee) { + log.warn("Can't add result '" + name + "' at step " + step, eee); + } + } + + protected void doAddResult(TimeStep step, String name, MatrixND mat, + TopiaContext tx) throws IsisFishException { + // si la matrice n'a pas de semantique on refuse + for (int i = 0; i < mat.getDimCount(); i++) { + // la semantique n'est pas bonne des qu'il y a un null dedans + if (mat.getSemantic(i).contains(null)) { + throw new SimulationException( + "Erreur le résultat que vous souhaitez enregistrer n'a pas d'information convenable pour la dimension: " + + i + " " + mat.getDimensionName(i)); + } + } + + // on fait une copie pour avoir reellement des resultats independant + // FIXME echatellier 20120829 : faire une copie optimiser + // suivant l'implementation du vector plutot qu'un parcourt + // via un iterateur de semantiques (plus couteux) + MatrixND newMat = mat.copy(); + try { + ResultDAO resultPS = IsisFishDAOHelper.getResultDAO(tx); + Result result = resultPS.create(); + result.setResultStep(step); + result.setName(name); + result.setMatrix(newMat); + resultPS.update(result); + + addAvailableResult(step, name); + putInCache(step, name, newMat, tx); + + // depuis isis fish 4.1.1, le commit est automatique à chaque + // résultat (gain de performance de 20% avec le clearCache) + tx.commitTransaction(); + // vide le cache hibernate. Sans cela, les resultats ne sont + // jamais supprimé du cache car la session n'est close + // qu'à la fin de la simulation + tx.clearCache(); + + // remove from cache result computed by #getMatrix(name) + // beacause, if a new step is added, result become false + // but DO NOT REMOVE result named step + name + removeInCache(name); + + } catch (TopiaException eee) { + log.warn("Can't add result '" + name + "' at step " + step, eee); + } + } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#addActiveRule(fr.ifremer.isisfish.types.TimeStep, fr.ifremer.isisfish.rule.Rule) + */ + @Override + public void addActiveRule(TimeStep step, Rule rule) throws IsisFishException { + try { + TopiaContext tx = null; + boolean mustClose = false; + + if (simulation == SimulationContext.get().getSimulationStorage()) { + tx = SimulationContext.get().getDbResult(); + } + if (tx == null) { + // not in simulation, create transaction + tx = simulation.getStorage().beginTransaction(); + mustClose = true; + } + ActiveRuleDAO ps = IsisFishDAOHelper.getActiveRuleDAO(tx); + ActiveRule result = ps.create(); + result.setActiveRuleStep(step); + result.setName(RuleStorage.getName(rule)); + result.setParam(RuleStorage.getParamAsString(rule)); + ps.update(result); + if (mustClose) { + tx.commitTransaction(); + tx.closeContext(); + } + } catch (TopiaException eee) { + throw new IsisFishException("Can't add result", eee); + } + } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#getResultName() + */ + @Override + public List<String> getResultName() { + + List<String> result = null; + try { + TopiaContext tx = null; + boolean mustClose = false; + + if (simulation == SimulationContext.get().getSimulationStorage()) { + tx = SimulationContext.get().getDbResult(); + } + if (tx == null) { + // not in simulation, create transaction + tx = simulation.getStorage().beginTransaction(); + mustClose = true; + } + ResultDAO resultPS = IsisFishDAOHelper.getResultDAO(tx); + + result = (List<String>) resultPS.getContext() + .findAll("Select distinct name from fr.ifremer.isisfish.entities.Result order by name"); + if (mustClose) { + tx.closeContext(); + } + } catch (TopiaException eee) { + if (log.isWarnEnabled()) { + log.warn("Can't get result name", eee); + } + } + if (result == null) { + result = new ArrayList<String>(); + } + return result; + } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#getMatrix(fr.ifremer.isisfish.types.TimeStep, fr.ifremer.isisfish.entities.Population, java.lang.String) + */ + @Override + public MatrixND getMatrix(TimeStep step, Population pop, String name) { + String newName = name + " " + pop; + return getMatrix(step, newName); + } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#getMatrix(fr.ifremer.isisfish.types.TimeStep, java.lang.String) + */ + @Override + public MatrixND getMatrix(TimeStep step, String name) { + MatrixND mat = getInCache(step, name); + if (mat == null && isAvailableResult(step, name)) { + try { + TopiaContext tx = null; + boolean mustClose = false; + + if (simulation == SimulationContext.get().getSimulationStorage()) { + tx = SimulationContext.get().getDbResult(); + } + if (tx == null) { + // not in simulation, create transaction + tx = simulation.getStorage().beginTransaction(); + mustClose = true; + } + mat = getMatrix(step, name, tx); + if (mustClose) { + // FIXME transaction never closed + // quand peut on fermer la transaction ? + // lorsque plus aucune matrice ne l'utilise. + // donc mettre la matrice et la connexion dans une map + // la matrice dans une weak reference. Des que la matrice + // est liberer faire un close sur la transaction + } else { + // echatellier 20120829 : vidage du cache hibernate + // sinon on fait trop de lecture que la meme transaction + // et le cache hibernate se remplit sans se vider + tx.clearCache(); + } + } catch (Exception eee) { + if (log.isWarnEnabled()) { + log.warn("Can't return matrix '" + name + "' for step " + + step, eee); + } + } + } + return mat; + } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#getMatrix(fr.ifremer.isisfish.types.TimeStep, java.lang.String, org.nuiton.topia.TopiaContext) + */ + @Override + public MatrixND getMatrix(TimeStep step, String name, TopiaContext tx) { + MatrixND mat = getInCache(step, name); + if (mat == null && isAvailableResult(step, name)) { + try { + ResultDAO resultPS = IsisFishDAOHelper.getResultDAO(tx); + Result result = resultPS.findByProperties( + Result.PROPERTY_RESULT_STEP, step, + Result.PROPERTY_NAME, name); + if (result != null) { + mat = result.getMatrix(); + putInCache(step, name, mat, tx); + } + } catch (Exception eee) { + if (log.isWarnEnabled()) { + log.warn("Can't return matrix '" + name + "' for step " + + step, eee); + } + } + } + return mat; + } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#getMatrix(fr.ifremer.isisfish.entities.Population, java.lang.String) + */ + @Override + public MatrixND getMatrix(Population pop, String name) { + String newName = name + " " + pop; + return getMatrix(newName); + } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#getMatrix(fr.ifremer.isisfish.entities.Population, java.lang.String, org.nuiton.topia.TopiaContext) + */ + @Override + public MatrixND getMatrix(Population pop, String name, TopiaContext tx) { + String newName = name + " " + pop; + return getMatrix(newName, tx); + } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#getMatrix(java.lang.String) + */ + @Override + public MatrixND getMatrix(String name) { + MatrixND resultMat = null; + try { + TopiaContext tx = null; + boolean mustClose = false; + + if (simulation == SimulationContext.get().getSimulationStorage()) { + tx = SimulationContext.get().getDbResult(); + } + if (tx == null) { + // not in simulation, create transaction + tx = simulation.getStorage().beginTransaction(); + mustClose = true; + } + resultMat = getMatrix(name, tx); + if (mustClose) { + // FIXME transaction never closed + // quand peut on fermer la transaction ? + // lorsque plus aucune matrice ne l'utilise. + // donc mettre la matrice et la connexion dans une map + // la matrice dans une weak reference. Des que la matrice + // est liberer faire un close sur la transaction + } else { + // echatellier 20120829 : vidage du cache hibernate + // sinon on fait trop de lecture que la meme transaction + // et le cache hibernate se remplit sans se vider + tx.clearCache(); + } + } catch (TopiaException eee) { + if (log.isWarnEnabled()) { + log.warn("Can't get result: " + name, eee); + } + } + return resultMat; + } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#getMatrix(java.lang.String, org.nuiton.topia.TopiaContext) + */ + @Override + public MatrixND getMatrix(String name, TopiaContext tx) { + log.debug("Get result: " + name); + + MatrixND resultMat = getInCache(name); + if (resultMat != null) { + return resultMat; + } + + // recuperation des resultats qui nous interesse + List<Result> results = null; + try { + ResultDAO resultPS = IsisFishDAOHelper.getResultDAO(tx); + results = resultPS.findAllByName(name); + } catch (TopiaException eee) { + if (log.isWarnEnabled()) { + log.warn("Can't get result: " + name, eee); + } + } + + // s'il n'y pas de resultat, on retourne null + if (results == null || results.size() == 0) { + return null; + } + + // Creation des listes pour chaque dimension + + // creation de la liste de date + TimeStep lastStep = getLastStep(); + List<TimeStep> steps = new ArrayList<TimeStep>(); + TimeStep step = new TimeStep(0); + steps.add(step); + while (step.before(lastStep)) { + step = step.next(); + steps.add(step); + } + + if (log.isTraceEnabled()) { + log.trace("Steps list : " + steps); + } + + // recuperation des dimensions des matrices + MatrixND mat = (MatrixND) results.get(0).getMatrix(); + + // recuperation des noms des dimensions + String[] dimNames = new String[1 + mat.getDimCount()]; + dimNames[0] = _("isisfish.common.date"); + for (int i = 1; i < dimNames.length; i++) { + dimNames[i] = mat.getDimensionName(i - 1); + } + + // creation de la semantique pour la matrice resultat. +1 pour les dates + List[] sem = new List[1 + mat.getDimCount()]; + sem[0] = steps; + + for (int i = 1; i < sem.length; i++) { + sem[i] = new HashList(); + } + + for (Result result : results) { + MatrixND mattmp = result.getMatrix(); + if (log.isTraceEnabled()) { + log.trace("Ajout de la semantics: " + + Arrays.asList(mattmp.getSemantics())); + } + + for (int s = 0; s < mattmp.getDimCount(); s++) { + sem[s + 1].addAll(mattmp.getSemantic(s)); + } + } + + if (log.isTraceEnabled()) { + log.trace("La semantique final est: " + Arrays.asList(sem)); + } + + // creation de la matrice resultat + resultMat = MatrixFactory.getInstance().create(name, sem, dimNames); + + // recuperation du resultat pour chaque date de la simulation, de Date(0) à lastDate + for (Result result : results) { + TimeStep d = result.getResultStep(); + mat = result.getMatrix(); + // on met ce resultat dans la matrice result si besoin + if (mat != null) { + // on recupere dans la matrice resultat l'endroit on il faut + // mettre la matrice + MatrixND submat = resultMat.getSubMatrix(0, d, 1); + // on met les valeur de mat dans la sous matrice extraite + for (MatrixIterator mi = mat.iterator(); mi.next();) { + submat.setValue( + ArrayUtil.concat(new Object[] { d }, + mi.getSemanticsCoordinates()), mi.getValue()); + } + } + } + + putInCache(name, resultMat, tx); + return resultMat; + } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#getLastStep() + */ + @Override + public TimeStep getLastStep() { + int monthNumber = simulation.getParameter().getNumberOfYear() + * Month.NUMBER_OF_MONTH; + TimeStep result = new TimeStep(monthNumber - 1); // -1 because date begin at 0 + return result; + } + + /* + * @see fr.ifremer.isisfish.simulator.SimulationResultListener#addResult(fr.ifremer.isisfish.simulator.SimulationContext, fr.ifremer.isisfish.types.TimeStep, java.lang.String, org.nuiton.math.matrix.MatrixND) + */ + @Override + public void addResult(SimulationContext context, TimeStep step, String name, + MatrixND mat) throws IsisFishException { + try { + doAddResult(step, name, mat, context.getDbResult()); + } catch (TopiaException eee) { + log.warn(_("Can't add result '%1$s' at date %2$s", name, step), eee); + } + } + + /* + * @see fr.ifremer.isisfish.simulator.SimulationResultGetter#getMatrix(fr.ifremer.isisfish.simulator.SimulationContext, fr.ifremer.isisfish.types.TimeStep, java.lang.String) + */ + @Override + public MatrixND getMatrix(SimulationContext context, TimeStep step, String name) { + MatrixND result = null; + try { + result = getMatrix(step, name, context.getDbResult()); + } catch (TopiaException eee) { + if (log.isWarnEnabled()) { + log.warn(_("Can't get result: %1$s", name), eee); + } + } + return result; + } + + /* + * @see fr.ifremer.isisfish.simulator.SimulationResultGetter#getMatrix(fr.ifremer.isisfish.simulator.SimulationContext, java.lang.String) + */ + @Override + public MatrixND getMatrix(SimulationContext context, String name) { + MatrixND result = null; + try { + result = getMatrix(name, context.getDbResult()); + } catch (TopiaException eee) { + if (log.isWarnEnabled()) { + log.warn(_("Can't get result: %1$s", name), eee); + } + } + return result; + } + + /* + * @see fr.ifremer.isisfish.simulator.SimulationListener#afterSimulation(fr.ifremer.isisfish.simulator.SimulationContext) + */ + @Override + public void afterSimulation(SimulationContext context) { + } + + /* + * @see fr.ifremer.isisfish.simulator.SimulationListener#beforeSimulation(fr.ifremer.isisfish.simulator.SimulationContext) + */ + @Override + public void beforeSimulation(SimulationContext context) { + } + + // public void addActivatedRule(ResultStorage self, Date date, RegleParam rule){ + // List rules = (List)activatedRules.get(date); + // if(rules == null){ + // activatedRules.put(date, rules = new LinkedList()); + // } + // rules.add(rule); + // } + + // /** + // * Retourne pour une date données tous les RegleParam qui ont été activé + // * a la date demandé. + // * @return une list de {@link fr.ifremer.nodb.RegleParam} + // */ + // public List getActivatedRule(ResultStorage self, Date date){ + // List rules = (List)activatedRules.get(date); + // if(rules == null){ + // activatedRules.put(date, rules = new LinkedList()); + // } + // return rules; + // } + +} // ResultDatabaseStorage Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java 2012-08-31 14:12:18 UTC (rev 3751) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java 2012-08-31 16:11:36 UTC (rev 3752) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2002 - 2011 Ifremer, Code Lutin, Cédric Pineau, Benjamin Poussin, Chatellier Eric + * Copyright (C) 2012 Ifremer, Code Lutin, Benjamin Poussin, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -83,7 +83,7 @@ * par : $Author$ */ public class ResultMappedStorage implements SimulationResultListener, - SimulationResultGetter { // ResultStorage + SimulationResultGetter, ResultStorage { // ResultStorage /** to use log facility, just put in your code: log.info(\"...\"); */ static private Log log = LogFactory.getLog(ResultMappedStorage.class); @@ -209,7 +209,6 @@ sems[i].add(s); } } - int size = (int) raf.getFilePointer(); int dataOffset = offset + size; @@ -602,6 +601,15 @@ String newName = name + " " + pop; return getMatrix(newName, null); } + + /* (non-Javadoc) + * @see fr.ifremer.isisfish.datastore.ResultStorage#getMatrix(fr.ifremer.isisfish.entities.Population, java.lang.String, org.nuiton.topia.TopiaContext) + */ + @Override + public MatrixND getMatrix(Population pop, String name, TopiaContext tx) { + String newName = name + " " + pop; + return getMatrix(newName, tx); + } /** * Retourne une matrice contenant tous les pas de temps. Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java 2012-08-31 14:12:18 UTC (rev 3751) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java 2012-08-31 16:11:36 UTC (rev 3752) @@ -1,214 +1,22 @@ -/* - * #%L - * IsisFish - * - * $Id$ - * $HeadURL$ - * %% - * Copyright (C) 2002 - 2011 Ifremer, Code Lutin, Cédric Pineau, 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 2 of the - * License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public - * License along with this program. If not, see - * <http://www.gnu.org/licenses/gpl-2.0.html>. - * #L% - */ - package fr.ifremer.isisfish.datastore; -import static org.nuiton.i18n.I18n._; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collection; -import java.util.HashSet; import java.util.List; -import java.util.Set; -import org.apache.commons.collections.map.ReferenceMap; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.hibernate.HibernateException; -import org.nuiton.math.matrix.MatrixFactory; -import org.nuiton.math.matrix.MatrixIterator; import org.nuiton.math.matrix.MatrixND; import org.nuiton.topia.TopiaContext; -import org.nuiton.topia.TopiaException; -import org.nuiton.topia.framework.TopiaContextImpl; -import org.nuiton.util.ArrayUtil; -import org.nuiton.util.HashList; -import fr.ifremer.isisfish.IsisFishDAOHelper; import fr.ifremer.isisfish.IsisFishException; -import fr.ifremer.isisfish.entities.ActiveRule; -import fr.ifremer.isisfish.entities.ActiveRuleDAO; import fr.ifremer.isisfish.entities.Population; -import fr.ifremer.isisfish.entities.Result; -import fr.ifremer.isisfish.entities.ResultDAO; import fr.ifremer.isisfish.export.Export; import fr.ifremer.isisfish.export.SensitivityExport; import fr.ifremer.isisfish.rule.Rule; -import fr.ifremer.isisfish.simulator.SimulationContext; -import fr.ifremer.isisfish.simulator.SimulationException; import fr.ifremer.isisfish.simulator.SimulationPlan; -import fr.ifremer.isisfish.simulator.SimulationResultGetter; import fr.ifremer.isisfish.simulator.SimulationResultListener; import fr.ifremer.isisfish.types.TimeStep; -import fr.ifremer.isisfish.types.Month; -/** - * Cette classe permet de conserver des résultats de simulation. Elle permet - * ensuite de les récupérer. - * - * Created: 29 sept. 2004 - * - * @author Benjamin Poussin <poussin(a)codelutin.com> - * @version $Revision$ - * - * Mise a jour: $Date$ - * par : $Author$ - */ -public class ResultStorage implements SimulationResultListener, - SimulationResultGetter { // ResultStorage +public interface ResultStorage extends SimulationResultListener { - /** to use log facility, just put in your code: log.info(\"...\"); */ - static private Log log = LogFactory.getLog(ResultStorage.class); - - protected SimulationStorage simulation = null; - // transient protected HashMap<String, MatrixND> globalMatrix = new HashMap<String, MatrixND>(); - transient protected ReferenceMap cacheContext = new ReferenceMap(ReferenceMap.HARD, ReferenceMap.WEAK); - - /** cache to maintains some result. key: String(date + ':' + name), value: matrix - * TODO: cache will be more efficient if it keep at min the number of result by year */ - transient protected ReferenceMap cache = new ReferenceMap(ReferenceMap.HARD, ReferenceMap.SOFT); - /** contains all available result as string: String(date + ':' + name) */ - transient protected Set<String> availableResult = null; - /** result enabled */ - transient protected Set<String> enabledResult = null; - /** - * Les ResultStorage ne doivent pas etre instancier directement, mais - * recuperer a partir d'un - * {@link fr.ifremer.isisfish.datastore.SimulationStorage#getResultStorage()} - * - * @param simulation storage to get result - */ - public ResultStorage(SimulationStorage simulation) { - this.simulation = simulation; - } - - protected void putInCache(TimeStep step, String name, MatrixND mat, TopiaContext context) { - String key = step.getStep() + ":" + name; - putInCache(key, mat, context); - } - - protected void putInCache(String name, MatrixND mat, TopiaContext context) { - if (mat != null) { - cache.put(name, mat); - cacheContext.put(name, context); - } - } - - /** - * Result can be removed from cache when computed result (from multiple step) - * become invalidated by new step result. - * - * @param name result name to remove - */ - protected void removeInCache(String name) { - cache.remove(name); - cacheContext.remove(name); - } - - protected MatrixND getInCache(TimeStep step, String name) { - // do not use toString for step (depend on i18n) - String key = step.getStep() + ":" + name; - MatrixND result = getInCache(key); - return result; - } - - protected MatrixND getInCache(String name) { - MatrixND result = null; - TopiaContext context = (TopiaContext) cacheContext.get(name); - if (context != null && !context.isClosed()) { - // on verifie que le context existe encore car on peut vouloir - // naviguer dans les semantics - result = (MatrixND) cache.get(name); - } - return result; - } - - /** - * Retourne le nom de tous les resultats disponibles le nom est constitué - * de la date et du nom du resultat. - * - * @return available results - */ - protected Set<String> getAvailableResult() { - if (availableResult == null) { - availableResult = new HashSet<String>(); - try { - TopiaContext tx = null; - boolean mustClose = false; - - if (simulation == SimulationContext.get().getSimulationStorage()) { - tx = SimulationContext.get().getDbResult(); - } - - if (tx == null) { - // not in simulation, create transaction - tx = simulation.getStorage().beginTransaction(); - mustClose = true; - } - - List<String> result = (List<String>) tx.findAll("Select " + Result.PROPERTY_RESULT_STEP + "||':'||name from fr.ifremer.isisfish.entities.Result"); - if (mustClose) { - tx.closeContext(); - } - availableResult.addAll(result); - } catch (Exception eee) { - if (log.isWarnEnabled()) { - log.warn("Can't get result available", eee); - } - } - } - return availableResult; - } - - /** - * Verifie si un resultat est disponible pour une date donnée. - * - * @param step - * @param name - * @return {@code true} if result is available - */ - protected boolean isAvailableResult(TimeStep step, String name) { - String key = step.getStep() + ":" + name; - boolean result = getAvailableResult().contains(key); - return result; - } - - /** - * Ajoute un resultat comme etant disponible pour une date donnée. - * - * @param step - * @param name - */ - protected void addAvailableResult(TimeStep step, String name) { - String key = step.getStep() + ":" + name; - getAvailableResult().add(key); - } - - /** * Permet de savoir si lorsque l'on ajoutera ce resultat, il sera * sauvé ou non. * @@ -223,241 +31,41 @@ * @param name result name * @return {@code true} if result is enabled */ - public boolean isEnabled(String name) { - name = name.trim(); - if (enabledResult == null) { - enabledResult = new HashSet<String>(); + public boolean isEnabled(String name); - Collection<String> resultEnabled = simulation.getParameter() - .getResultEnabled(); - enabledResult.addAll(resultEnabled); + public void addResult(TimeStep step, MatrixND mat) throws IsisFishException; - // test on export - List<String> exportNames = simulation.getParameter().getExportNames(); - if (exportNames != null) { - for (String exportName : exportNames) { - ExportStorage storage = ExportStorage.getExport(exportName); - try { - Export export = storage.getNewExportInstance(); - for (String resultName : export.getNecessaryResult()) { - enabledResult.add(resultName); - } - } catch (IsisFishException eee) { - if (log.isWarnEnabled()) { - log.warn(_("isisfish.error.instanciate.export", - exportName), eee); - } - } - } - } + public void addResult(TimeStep step, Population pop, MatrixND mat) + throws IsisFishException; - // test on sensitivity export - List<SensitivityExport> sensitivityExports = simulation - .getParameter().getSensitivityExport(); - if (sensitivityExports != null) { - for (SensitivityExport sensitivityExport : sensitivityExports) { - for (String resultName : sensitivityExport.getNecessaryResult()) { - enabledResult.add(resultName); - } - } - } + public void addResult(boolean force, TimeStep step, MatrixND mat) + throws IsisFishException; - // test on rules - List<Rule> rules = simulation.getParameter().getRules(); - if (rules != null) { - for (Rule rule : rules) { - for (String resultName : rule.getNecessaryResult()) { - enabledResult.add(resultName); - } - } - } + public void addResult(boolean force, TimeStep step, Population pop, + MatrixND mat) throws IsisFishException; - // test on plans - List<SimulationPlan> plans = simulation.getParameter().getSimulationPlans(); - if (plans != null) { - for (SimulationPlan plan : plans) { - for (String resultName : plan.getNecessaryResult()) { - enabledResult.add(resultName); - } - } - } - log.info("Enabled result: " + enabledResult); - } - boolean result = enabledResult.contains(name); - return result; - } + public void addResult(TimeStep step, String name, Population pop, + MatrixND mat) throws IsisFishException; - public void addResult(TimeStep step, MatrixND mat) throws IsisFishException { - addResult(false, step, mat.getName(), mat); - } + public void addResult(TimeStep step, String name, MatrixND mat) + throws IsisFishException; - public void addResult(TimeStep step, Population pop, MatrixND mat) throws IsisFishException { - addResult(false, step, mat.getName(), pop, mat); - } + public void addResult(boolean force, TimeStep step, String name, + Population pop, MatrixND mat) throws IsisFishException; - public void addResult(boolean force, TimeStep step, MatrixND mat) throws IsisFishException { - addResult(force, step, mat.getName(), mat); - } + public void addResult(boolean force, TimeStep step, String name, + MatrixND mat) throws IsisFishException; - public void addResult(boolean force, TimeStep step, Population pop, MatrixND mat) throws IsisFishException { - addResult(force, step, mat.getName(), pop, mat); - } + public void addActiveRule(TimeStep step, Rule rule) + throws IsisFishException; - public void addResult(TimeStep step, String name, Population pop, MatrixND mat) throws IsisFishException { - addResult(false, step, name, pop, mat); - } - - public void addResult(TimeStep step, String name, MatrixND mat) throws IsisFishException { - addResult(false, step, name, mat); - } - - public void addResult(boolean force, TimeStep step, String name, Population pop, MatrixND mat) throws IsisFishException { - if (force || isEnabled(name)) { - doAddResult(step, name + " " + pop, mat); - } - } - - public void addResult(boolean force, TimeStep step, String name, MatrixND mat) throws IsisFishException { - if (force || isEnabled(name)) { - doAddResult(step, name, mat); - } - } - - protected void doAddResult(TimeStep step, String name, MatrixND mat) throws IsisFishException { - try { - TopiaContext tx = null; - boolean mustClose = false; - - if (simulation == SimulationContext.get().getSimulationStorage()) { - tx = SimulationContext.get().getDbResult(); - } - if (tx == null) { - // not in simulation, create transaction - tx = simulation.getStorage().beginTransaction(); - mustClose = true; - } - doAddResult(step, name, mat, tx); - if (mustClose) { - tx.commitTransaction(); - tx.closeContext(); - } - } catch (TopiaException eee) { - log.warn("Can't add result '" + name + "' at step " + step, eee); - } - } - - protected void doAddResult(TimeStep step, String name, MatrixND mat, - TopiaContext tx) throws IsisFishException { - // si la matrice n'a pas de semantique on refuse - for (int i = 0; i < mat.getDimCount(); i++) { - // la semantique n'est pas bonne des qu'il y a un null dedans - if (mat.getSemantic(i).contains(null)) { - throw new SimulationException( - "Erreur le résultat que vous souhaitez enregistrer n'a pas d'information convenable pour la dimension: " - + i + " " + mat.getDimensionName(i)); - } - } - - // on fait une copie pour avoir reellement des resultats independant - // FIXME echatellier 20120829 : faire une copie optimiser - // suivant l'implementation du vector plutot qu'un parcourt - // via un iterateur de semantiques (plus couteux) - MatrixND newMat = mat.copy(); - try { - ResultDAO resultPS = IsisFishDAOHelper.getResultDAO(tx); - Result result = resultPS.create(); - result.setResultStep(step); - result.setName(name); - result.setMatrix(newMat); - resultPS.update(result); - - addAvailableResult(step, name); - putInCache(step, name, newMat, tx); - - // depuis isis fish 4.1.1, le commit est automatique à chaque - // résultat (gain de performance de 20% avec le clearCache) - tx.commitTransaction(); - // vide le cache hibernate. Sans cela, les resultats ne sont - // jamais supprimé du cache car la session n'est close - // qu'à la fin de la simulation - tx.clearCache(); - - // remove from cache result computed by #getMatrix(name) - // beacause, if a new step is added, result become false - // but DO NOT REMOVE result named step + name - removeInCache(name); - - } catch (TopiaException eee) { - log.warn("Can't add result '" + name + "' at step " + step, eee); - } - } - - public void addActiveRule(TimeStep step, Rule rule) throws IsisFishException { - try { - TopiaContext tx = null; - boolean mustClose = false; - - if (simulation == SimulationContext.get().getSimulationStorage()) { - tx = SimulationContext.get().getDbResult(); - } - if (tx == null) { - // not in simulation, create transaction - tx = simulation.getStorage().beginTransaction(); - mustClose = true; - } - ActiveRuleDAO ps = IsisFishDAOHelper.getActiveRuleDAO(tx); - ActiveRule result = ps.create(); - result.setActiveRuleStep(step); - result.setName(RuleStorage.getName(rule)); - result.setParam(RuleStorage.getParamAsString(rule)); - ps.update(result); - if (mustClose) { - tx.commitTransaction(); - tx.closeContext(); - } - } catch (TopiaException eee) { - throw new IsisFishException("Can't add result", eee); - } - } - /** * Retourne la liste de tous les résultats. Si le résultat est categorisé * par une population alors le nom de la population est automatiquement * ajouté au nom du résultat. */ - public List<String> getResultName() { + public List<String> getResultName(); - List<String> result = null; - try { - TopiaContext tx = null; - boolean mustClose = false; - - if (simulation == SimulationContext.get().getSimulationStorage()) { - tx = SimulationContext.get().getDbResult(); - } - if (tx == null) { - // not in simulation, create transaction - tx = simulation.getStorage().beginTransaction(); - mustClose = true; - } - ResultDAO resultPS = IsisFishDAOHelper.getResultDAO(tx); - - result = (List<String>) resultPS.getContext() - .findAll("Select distinct name from fr.ifremer.isisfish.entities.Result order by name"); - if (mustClose) { - tx.closeContext(); - } - } catch (TopiaException eee) { - if (log.isWarnEnabled()) { - log.warn("Can't get result name", eee); - } - } - if (result == null) { - result = new ArrayList<String>(); - } - return result; - } - /** * Retourne la matrice stocke pour un pas de temps * @param step le pas de temps que l'on souhaite @@ -466,50 +74,10 @@ * @return La matrice demandée ou null si aucune matrice ne correspond a * la demande. */ - public MatrixND getMatrix(TimeStep step, Population pop, String name) { - String newName = name + " " + pop; - return getMatrix(step, newName); - } + public MatrixND getMatrix(TimeStep step, Population pop, String name); - public MatrixND getMatrix(TimeStep step, String name) { - MatrixND mat = getInCache(step, name); - if (mat == null && isAvailableResult(step, name)) { - try { - TopiaContext tx = null; - boolean mustClose = false; + public MatrixND getMatrix(TimeStep step, String name); - if (simulation == SimulationContext.get().getSimulationStorage()) { - tx = SimulationContext.get().getDbResult(); - } - if (tx == null) { - // not in simulation, create transaction - tx = simulation.getStorage().beginTransaction(); - mustClose = true; - } - mat = getMatrix(step, name, tx); - if (mustClose) { - // FIXME transaction never closed - // quand peut on fermer la transaction ? - // lorsque plus aucune matrice ne l'utilise. - // donc mettre la matrice et la connexion dans une map - // la matrice dans une weak reference. Des que la matrice - // est liberer faire un close sur la transaction - } else { - // echatellier 20120829 : vidage du cache hibernate - // sinon on fait trop de lecture que la meme transaction - // et le cache hibernate se remplit sans se vider - tx.clearCache(); - } - } catch (Exception eee) { - if (log.isWarnEnabled()) { - log.warn("Can't return matrix '" + name + "' for step " - + step, eee); - } - } - } - return mat; - } - /** * Retourne la matrice stocke pour un pas de temps. * @@ -519,37 +87,14 @@ * @return La matrice demandée ou {@code null} si aucune matrice ne correspond a * la demande. */ - public MatrixND getMatrix(TimeStep step, String name, TopiaContext tx) { - MatrixND mat = getInCache(step, name); - if (mat == null && isAvailableResult(step, name)) { - try { - ResultDAO resultPS = IsisFishDAOHelper.getResultDAO(tx); - Result result = resultPS.findByProperties( - Result.PROPERTY_RESULT_STEP, step, - Result.PROPERTY_NAME, name); - if (result != null) { - mat = result.getMatrix(); - putInCache(step, name, mat, tx); - } - } catch (Exception eee) { - if (log.isWarnEnabled()) { - log.warn("Can't return matrix '" + name + "' for step " - + step, eee); - } - } - } - return mat; - } + public MatrixND getMatrix(TimeStep step, String name, TopiaContext tx); /** * Retourne une matrice contenant tous les pas de temps. * @param pop la population pour lequel on souhaite la matrice * @param name le nom des resultats dont on veut une matrice globale. */ - public MatrixND getMatrix(Population pop, String name) { - String newName = name + " " + pop; - return getMatrix(newName); - } + public MatrixND getMatrix(Population pop, String name); /** * Retourne une matrice contenant tous les pas de temps. @@ -558,245 +103,25 @@ * @param tx la transaction a utiliser * @since 4.1.0.0 */ - public MatrixND getMatrix(Population pop, String name, TopiaContext tx) { - String newName = name + " " + pop; - return getMatrix(newName, tx); - } + public MatrixND getMatrix(Population pop, String name, TopiaContext tx); /** * Retourne une matrice contenant tous les pas de temps. * @param name le nom des resultats dont on veut une matrice globale. */ - public MatrixND getMatrix(String name) { - MatrixND resultMat = null; - try { - TopiaContext tx = null; - boolean mustClose = false; + public MatrixND getMatrix(String name); - if (simulation == SimulationContext.get().getSimulationStorage()) { - tx = SimulationContext.get().getDbResult(); - } - if (tx == null) { - // not in simulation, create transaction - tx = simulation.getStorage().beginTransaction(); - mustClose = true; - } - resultMat = getMatrix(name, tx); - if (mustClose) { - // FIXME transaction never closed - // quand peut on fermer la transaction ? - // lorsque plus aucune matrice ne l'utilise. - // donc mettre la matrice et la connexion dans une map - // la matrice dans une weak reference. Des que la matrice - // est liberer faire un close sur la transaction - } else { - // echatellier 20120829 : vidage du cache hibernate - // sinon on fait trop de lecture que la meme transaction - // et le cache hibernate se remplit sans se vider - tx.clearCache(); - } - } catch (TopiaException eee) { - if (log.isWarnEnabled()) { - log.warn("Can't get result: " + name, eee); - } - } - return resultMat; - } - /** * Retourne une matrice contenant tous les pas de temps. * @param name le nom des resultats dont on veut une matrice globale. * @param tx TopiaContext a utiliser pour recuperer les resultats et donc les semantiques */ - public MatrixND getMatrix(String name, TopiaContext tx) { - log.debug("Get result: " + name); + public MatrixND getMatrix(String name, TopiaContext tx); - MatrixND resultMat = getInCache(name); - if (resultMat != null) { - return resultMat; - } - - // recuperation des resultats qui nous interesse - List<Result> results = null; - try { - ResultDAO resultPS = IsisFishDAOHelper.getResultDAO(tx); - results = resultPS.findAllByName(name); - } catch (TopiaException eee) { - if (log.isWarnEnabled()) { - log.warn("Can't get result: " + name, eee); - } - } - - // s'il n'y pas de resultat, on retourne null - if (results == null || results.size() == 0) { - return null; - } - - // Creation des listes pour chaque dimension - - // creation de la liste de date - TimeStep lastStep = getLastStep(); - List<TimeStep> steps = new ArrayList<TimeStep>(); - TimeStep step = new TimeStep(0); - steps.add(step); - while (step.before(lastStep)) { - step = step.next(); - steps.add(step); - } - - if (log.isTraceEnabled()) { - log.trace("Steps list : " + steps); - } - - // recuperation des dimensions des matrices - MatrixND mat = (MatrixND) results.get(0).getMatrix(); - - // recuperation des noms des dimensions - String[] dimNames = new String[1 + mat.getDimCount()]; - dimNames[0] = _("isisfish.common.date"); - for (int i = 1; i < dimNames.length; i++) { - dimNames[i] = mat.getDimensionName(i - 1); - } - - // creation de la semantique pour la matrice resultat. +1 pour les dates - List[] sem = new List[1 + mat.getDimCount()]; - sem[0] = steps; - - for (int i = 1; i < sem.length; i++) { - sem[i] = new HashList(); - } - - for (Result result : results) { - MatrixND mattmp = result.getMatrix(); - if (log.isTraceEnabled()) { - log.trace("Ajout de la semantics: " - + Arrays.asList(mattmp.getSemantics())); - } - - for (int s = 0; s < mattmp.getDimCount(); s++) { - sem[s + 1].addAll(mattmp.getSemantic(s)); - } - } - - if (log.isTraceEnabled()) { - log.trace("La semantique final est: " + Arrays.asList(sem)); - } - - // creation de la matrice resultat - resultMat = MatrixFactory.getInstance().create(name, sem, dimNames); - - // recuperation du resultat pour chaque date de la simulation, de Date(0) à lastDate - for (Result result : results) { - TimeStep d = result.getResultStep(); - mat = result.getMatrix(); - // on met ce resultat dans la matrice result si besoin - if (mat != null) { - // on recupere dans la matrice resultat l'endroit on il faut - // mettre la matrice - MatrixND submat = resultMat.getSubMatrix(0, d, 1); - // on met les valeur de mat dans la sous matrice extraite - for (MatrixIterator mi = mat.iterator(); mi.next();) { - submat.setValue( - ArrayUtil.concat(new Object[] { d }, - mi.getSemanticsCoordinates()), mi.getValue()); - } - } - } - - putInCache(name, resultMat, tx); - return resultMat; - } - /** * Get last simulation date. * * @return last simulation date */ - public TimeStep getLastStep() { - int monthNumber = simulation.getParameter().getNumberOfYear() - * Month.NUMBER_OF_MONTH; - TimeStep result = new TimeStep(monthNumber - 1); // -1 because date begin at 0 - return result; - } - - /* - * @see fr.ifremer.isisfish.simulator.SimulationResultListener#addResult(fr.ifremer.isisfish.simulator.SimulationContext, fr.ifremer.isisfish.types.TimeStep, java.lang.String, org.nuiton.math.matrix.MatrixND) - */ - @Override - public void addResult(SimulationContext context, TimeStep step, String name, - MatrixND mat) throws IsisFishException { - try { - doAddResult(step, name, mat, context.getDbResult()); - } catch (TopiaException eee) { - log.warn(_("Can't add result '%1$s' at date %2$s", name, step), eee); - } - } - - /* - * @see fr.ifremer.isisfish.simulator.SimulationResultGetter#getMatrix(fr.ifremer.isisfish.simulator.SimulationContext, fr.ifremer.isisfish.types.TimeStep, java.lang.String) - */ - @Override - public MatrixND getMatrix(SimulationContext context, TimeStep step, String name) { - MatrixND result = null; - try { - result = getMatrix(step, name, context.getDbResult()); - } catch (TopiaException eee) { - if (log.isWarnEnabled()) { - log.warn(_("Can't get result: %1$s", name), eee); - } - } - return result; - } - - /* - * @see fr.ifremer.isisfish.simulator.SimulationResultGetter#getMatrix(fr.ifremer.isisfish.simulator.SimulationContext, java.lang.String) - */ - @Override - public MatrixND getMatrix(SimulationContext context, String name) { - MatrixND result = null; - try { - result = getMatrix(name, context.getDbResult()); - } catch (TopiaException eee) { - if (log.isWarnEnabled()) { - log.warn(_("Can't get result: %1$s", name), eee); - } - } - return result; - } - - /* - * @see fr.ifremer.isisfish.simulator.SimulationListener#afterSimulation(fr.ifremer.isisfish.simulator.SimulationContext) - */ - @Override - public void afterSimulation(SimulationContext context) { - } - - /* - * @see fr.ifremer.isisfish.simulator.SimulationListener#beforeSimulation(fr.ifremer.isisfish.simulator.SimulationContext) - */ - @Override - public void beforeSimulation(SimulationContext context) { - } - - // public void addActivatedRule(ResultStorage self, Date date, RegleParam rule){ - // List rules = (List)activatedRules.get(date); - // if(rules == null){ - // activatedRules.put(date, rules = new LinkedList()); - // } - // rules.add(rule); - // } - - // /** - // * Retourne pour une date données tous les RegleParam qui ont été activé - // * a la date demandé. - // * @return une list de {@link fr.ifremer.nodb.RegleParam} - // */ - // public List getActivatedRule(ResultStorage self, Date date){ - // List rules = (List)activatedRules.get(date); - // if(rules == null){ - // activatedRules.put(date, rules = new LinkedList()); - // } - // return rules; - // } - -} // ResultStorage + public TimeStep getLastStep(); +} Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java 2012-08-31 14:12:18 UTC (rev 3751) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java 2012-08-31 16:11:36 UTC (rev 3752) @@ -444,15 +444,20 @@ } /** - * Get simulation {@link ResultStorage}. + * Get simulation {@link ResultDatabaseStorage}. * - * @return le {@link ResultStorage} a utiliser pour cette simulation + * @return le {@link ResultDatabaseStorage} a utiliser pour cette simulation + * @throws StorageException */ - public ResultStorage getResultStorage() { + public ResultStorage getResultStorage() throws StorageException { if (resultStorage == null) { - // FIXME poussin 20120831 en fonction de la version de la base // instancier un ResultStorage ou un ResultMappedStorage - resultStorage = new ResultStorage(this); + //resultStorage = new ResultDatabaseStorage(this); + try { + resultStorage = new ResultMappedStorage(this); + } catch (IOException ex) { + throw new StorageException("Can't get storage", ex); + } } return resultStorage; }

1 0

r3751 - in trunk/src/main: java/fr/ifremer/isisfish/mexico java/fr/ifremer/isisfish/ui/sensitivity resources/i18n
by echatellier＠users.forge.codelutin.com 31 Aug '12

31 Aug '12

Author: echatellier Date: 2012-08-31 16:12:18 +0200 (Fri, 31 Aug 2012) New Revision: 3751 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3751 Log: fixes #1450 : Add option to export factor list into mexico xml file Modified: trunk/src/main/java/fr/ifremer/isisfish/mexico/MexicoHelper.java trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/SensitivityInputHandler.java trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/SensitivityTabUI.jaxx trunk/src/main/resources/i18n/isis-fish_en_GB.properties trunk/src/main/resources/i18n/isis-fish_fr_FR.properties Modified: trunk/src/main/java/fr/ifremer/isisfish/mexico/MexicoHelper.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/mexico/MexicoHelper.java 2012-08-31 13:09:22 UTC (rev 3750) +++ trunk/src/main/java/fr/ifremer/isisfish/mexico/MexicoHelper.java 2012-08-31 14:12:18 UTC (rev 3751) @@ -45,6 +45,8 @@ import org.apache.commons.beanutils.BeanUtils; import org.apache.commons.beanutils.ConvertUtilsBean; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.FilenameUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringEscapeUtils; import org.apache.commons.logging.Log; @@ -59,6 +61,7 @@ import org.nuiton.topia.TopiaContext; import org.nuiton.topia.persistence.TopiaDAO; import org.nuiton.topia.persistence.TopiaEntity; +import org.omg.CosNaming.NamingContextExtPackage.StringNameHelper; import org.xml.sax.InputSource; import fr.ifremer.isisfish.IsisFishDAOHelper; @@ -106,7 +109,20 @@ designPlanXml = MexicoHelper.formatXML(designPlanXml); return designPlanXml; + } + /** + * Convert design plan to xml and write it to given file. + * + * @param designPlan + */ + public static void writeDesignPlanToFile(File file, DesignPlan designPlan) { + String content = getDesignPlanAsXML(designPlan); + try { + FileUtils.writeStringToFile(file, content); + } catch (IOException ex) { + throw new IsisFishRuntimeException("Can't export factors to xml file", ex); + } } /** Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/SensitivityInputHandler.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/SensitivityInputHandler.java 2012-08-31 13:09:22 UTC (rev 3750) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/SensitivityInputHandler.java 2012-08-31 14:12:18 UTC (rev 3751) @@ -29,6 +29,8 @@ import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.MouseEvent; +import java.io.File; +import java.io.IOException; import java.lang.reflect.Method; import java.util.ArrayList; import java.util.List; @@ -51,6 +53,8 @@ import jaxx.runtime.context.JAXXInitialContext; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.FilenameUtils; import org.apache.commons.lang3.ArrayUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; @@ -61,12 +65,15 @@ import org.nuiton.topia.TopiaException; import org.nuiton.topia.persistence.TopiaEntity; import org.nuiton.topia.persistence.TopiaEntityContextable; +import org.nuiton.util.FileUtil; import fr.ifremer.isisfish.IsisFishRuntimeException; import fr.ifremer.isisfish.datastore.RegionStorage; import fr.ifremer.isisfish.entities.Equation; import fr.ifremer.isisfish.entities.FisheryRegion; +import fr.ifremer.isisfish.mexico.MexicoHelper; import fr.ifremer.isisfish.rule.Rule; +import fr.ifremer.isisfish.simulator.sensitivity.DesignPlan; import fr.ifremer.isisfish.simulator.sensitivity.Domain; import fr.ifremer.isisfish.simulator.sensitivity.Factor; import fr.ifremer.isisfish.simulator.sensitivity.FactorGroup; @@ -91,8 +98,8 @@ import fr.ifremer.isisfish.ui.input.tree.FisheryTreeRenderer; import fr.ifremer.isisfish.ui.simulator.RuleChooser; import fr.ifremer.isisfish.ui.simulator.SimulAction; +import fr.ifremer.isisfish.ui.widget.editor.MonthComponent; import fr.ifremer.isisfish.ui.widget.editor.StepComponent; -import fr.ifremer.isisfish.ui.widget.editor.MonthComponent; /** * Handler for sensitivity tab ui (fishery region factors). @@ -1266,4 +1273,33 @@ factorWizardUI.getContextValue(SimulationUI.class, "SimulationUI").refreshFactorTree(); factorWizardUI.dispose(); } + + /** + * Export factors list to xml mexico file. + * + * @since 4.1.1.2 + */ + public void exportFactorsToMexico(SensitivityTabUI view) { + File xmlFile = FileUtil.getFile(_("isisfish.sensitivity.mexico.exporttoxml.title"), + _("isisfish.sensitivity.mexico.exporttoxml.approve"), view, + new String[]{ + ".*\\.xml", + _("isisfish.sensitivity.mexico.exporttoxml.filter") + }); + + if (xmlFile != null) { + + // try to add ".xml" extension if no present + if (!FilenameUtils.isExtension(xmlFile.getAbsolutePath(), "xml")) { + xmlFile = new File(xmlFile.getAbsolutePath() + ".xml"); + } + + SimulAction simulAction = view.getContextValue(SimulAction.class); + + DesignPlan designPlan = new DesignPlan(); + designPlan.setFactorGroup(simulAction.getFactorGroup()); + String xml = MexicoHelper.getDesignPlanAsXML(designPlan); + MexicoHelper.writeDesignPlanToFile(xmlFile, designPlan); + } + } } Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/SensitivityTabUI.jaxx =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/SensitivityTabUI.jaxx 2012-08-31 13:09:22 UTC (rev 3750) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/SensitivityTabUI.jaxx 2012-08-31 14:12:18 UTC (rev 3751) @@ -108,13 +108,17 @@ <JButton icon="factors/dgroup.png" toolTipText="isisfish.sensitivity.newfactordgroup.tip" onActionPerformed="getHandler().addNewFactorGroup(this, false)"/> </cell> - <cell anchor='west' weightx='1'> + <cell anchor='west'> <JButton icon="factors/cgroup.png" toolTipText="isisfish.sensitivity.newfactorcgroup.tip" onActionPerformed="getHandler().addNewFactorGroup(this, true)"/> </cell> + <cell anchor='west' weightx='1'> + <JButton icon="script_go.png" toolTipText="isisfish.sensitivity.mexico.exporttoxml.tip" + onActionPerformed="getHandler().exportFactorsToMexico(this)"/> + </cell> </row> <row> - <cell columns='2' fill="both" weightx='1.0' weighty='1.0'> + <cell columns='3' fill="both" weightx='1.0' weighty='1.0'> <JScrollPane> <FactorTree id="factorsTree" constructorParams='this' rootVisible="true" selectionRow='0' Modified: trunk/src/main/resources/i18n/isis-fish_en_GB.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2012-08-31 13:09:22 UTC (rev 3750) +++ trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2012-08-31 14:12:18 UTC (rev 3751) @@ -866,6 +866,10 @@ isisfish.sensitivity.increment=Cardinality isisfish.sensitivity.lastValue=Last value isisfish.sensitivity.methodfactorsupported=The selected sensitivity method handles factors cardinalities +isisfish.sensitivity.mexico.exporttoxml.approve=Export +isisfish.sensitivity.mexico.exporttoxml.filter=Xml files +isisfish.sensitivity.mexico.exporttoxml.tip=Export factors to mexico xml file +isisfish.sensitivity.mexico.exporttoxml.title=Export factors to mexico xml file isisfish.sensitivity.moveillegal=Can't move discrete factor to continuous group \! isisfish.sensitivity.name=Factor name isisfish.sensitivity.newfactorcgroup.tip=Add new continuous factor group Modified: trunk/src/main/resources/i18n/isis-fish_fr_FR.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2012-08-31 13:09:22 UTC (rev 3750) +++ trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2012-08-31 14:12:18 UTC (rev 3751) @@ -866,6 +866,10 @@ isisfish.sensitivity.increment=Cardinalité isisfish.sensitivity.lastValue=Dernière valeur isisfish.sensitivity.methodfactorsupported=La méthode de sensibilité choisie gère les cardinalités des facteurs +isisfish.sensitivity.mexico.exporttoxml.approve=Exporter +isisfish.sensitivity.mexico.exporttoxml.filter=Fichier XML +isisfish.sensitivity.mexico.exporttoxml.tip=Exporter les facteurs vers un fichier xml mexico +isisfish.sensitivity.mexico.exporttoxml.title=Exporter les facteurs vers un fichier xml mexico isisfish.sensitivity.moveillegal=Impossible d'ajouter un facteur discret dans un groupe continu \! isisfish.sensitivity.name=Nom du facteur isisfish.sensitivity.newfactorcgroup.tip=Ajouter un groupe de facteur continu

1 0

r3750 - in trunk: . src/main/java/fr/ifremer/isisfish/datastore
by bpoussin＠users.forge.codelutin.com 31 Aug '12

31 Aug '12

Author: bpoussin Date: 2012-08-31 15:09:22 +0200 (Fri, 31 Aug 2012) New Revision: 3750 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3750 Log: ajout de l'implantation d'un ResultStorage sur un RandomAccessFile Added: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java Modified: trunk/pom.xml trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-08-30 14:46:24 UTC (rev 3749) +++ trunk/pom.xml 2012-08-31 13:09:22 UTC (rev 3750) @@ -62,7 +62,7 @@ <dependency> <groupId>org.nuiton.matrix</groupId> <artifactId>nuiton-matrix</artifactId> - <version>2.3.1</version> + <version>2.3.2-SNAPSHOT</version> <scope>compile</scope> </dependency> Copied: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java (from rev 3749, trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java) =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java (rev 0) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java 2012-08-31 13:09:22 UTC (rev 3750) @@ -0,0 +1,792 @@ +/* + * #%L + * IsisFish + * + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2002 - 2011 Ifremer, Code Lutin, Cédric Pineau, 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 2 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-2.0.html>. + * #L% + */ + +package fr.ifremer.isisfish.datastore; + +import fr.ifremer.isisfish.IsisFishDAOHelper; +import fr.ifremer.isisfish.IsisFishException; +import fr.ifremer.isisfish.entities.ActiveRule; +import fr.ifremer.isisfish.entities.ActiveRuleDAO; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.export.Export; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.rule.Rule; +import fr.ifremer.isisfish.simulator.SimulationContext; +import fr.ifremer.isisfish.simulator.SimulationException; +import fr.ifremer.isisfish.simulator.SimulationPlan; +import fr.ifremer.isisfish.simulator.SimulationResultGetter; +import fr.ifremer.isisfish.simulator.SimulationResultListener; +import fr.ifremer.isisfish.types.Month; +import fr.ifremer.isisfish.types.TimeStep; +import java.io.File; +import java.io.IOException; +import java.io.RandomAccessFile; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.Collections; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.TreeMap; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.nuiton.math.matrix.DoubleBigMappedVector; +import org.nuiton.math.matrix.MatrixFactory; +import org.nuiton.math.matrix.MatrixHelper; +import org.nuiton.math.matrix.MatrixIterator; +import org.nuiton.math.matrix.MatrixND; +import org.nuiton.math.matrix.MatrixSemanticsDecorator; +import org.nuiton.math.matrix.SemanticsDecorator; +import org.nuiton.topia.TopiaContext; +import org.nuiton.topia.TopiaException; +import org.nuiton.topia.persistence.TopiaEntity; +import org.nuiton.util.ArrayUtil; +import org.nuiton.util.HashList; + +import static org.nuiton.i18n.I18n._; + +/** + * Cette classe permet de conserver des résultats de simulation. Elle permet + * ensuite de les récupérer. + * + * Created: 31 aout 2012 + * + * @author Benjamin Poussin <poussin(a)codelutin.com> + * @version $Revision$ + * + * Mise a jour: $Date$ + * par : $Author$ + */ +public class ResultMappedStorage implements SimulationResultListener, + SimulationResultGetter { // ResultStorage + + /** to use log facility, just put in your code: log.info(\"...\"); */ + static private Log log = LogFactory.getLog(ResultMappedStorage.class); + + static protected MatrixFactory matrixFactory = MatrixFactory.getInstance(DoubleBigMappedVector.class); + + protected SimulationStorage simulation = null; + protected RandomAccessFile raf; + protected int offset; + protected Map<TimeStep, Map<String, ResultMapped>> stepNameResults = + new TreeMap<TimeStep, Map<String, ResultMapped>>(); + protected Map<String, Map<TimeStep, ResultMapped>> nameStepResults = + new TreeMap<String, Map<TimeStep, ResultMapped>>(); + + /** result enabled */ + transient protected Set<String> enabledResult = null; + + /** + * Convertie une entite, month, timestep en string et inversement. + * Entity = "TopiaId:Entity.toString" + */ + static protected class EntitySemanticsDecorator implements SemanticsDecorator { + static final private String SEP = ":"; + + protected TopiaContext tx; + + public EntitySemanticsDecorator() { + } + + public EntitySemanticsDecorator(TopiaContext tx) { + this.tx = tx; + } + + public Object decorate(Object internalValue) { + Object result = internalValue; + if (internalValue instanceof String) { + if (StringUtils.startsWith((String)internalValue, Month.class.getName())) { + String val = StringUtils.substringAfter((String)internalValue, SEP); + int monthNumber = Integer.parseInt(val); + result = new Month(monthNumber); + } else if (StringUtils.startsWith((String)internalValue, TimeStep.class.getName())) { + String val = StringUtils.substringAfter((String)internalValue, SEP); + int stepNumber = Integer.parseInt(val); + result = new TimeStep(stepNumber); + } else if (StringUtils.startsWith((String)internalValue, "fr.ifremer.isisfish.entities.")) { + if (tx == null) { + result = StringUtils.substringAfter((String)internalValue, SEP); + } else { + try { + String id = StringUtils.substringBefore((String)internalValue, SEP); + result = tx.findByTopiaId(id); + } catch (TopiaException eee) { + log.info("Fallback use string representation because" + + " i can't decorate (String->Entity): " + + internalValue, eee); + // si on arrive pas a convertir cette fois-ci, on + // renvoi internalValue pour que le undecorate est toutes les infos + // et donc que la prochaine fois on y arrive peut etre + } + } + } + } + return result; + } + + public Object undecorate(Object decoratedValue) { + String result; + if (decoratedValue instanceof Month) { + result = Month.class.getName() + SEP + ((Month)decoratedValue).getMonthNumber(); + } else if (decoratedValue instanceof TimeStep) { + result = TimeStep.class.getName() + SEP + ((TimeStep)decoratedValue).getStep(); + } else if (decoratedValue instanceof TopiaEntity) { + result = ((TopiaEntity)decoratedValue).getTopiaId() + SEP + decoratedValue; + } else { + result = String.valueOf(decoratedValue); + } + return result; + } + + } + + /** + * Represente un resultat + * Lors de la construction, si on ne passe que le RandomAccessFile et l'offset, on relie un resultat + * si on passe toutes les infos, on ecrit le resultat. + * Les deux operations doivent etre symetrique on lit et ecrit les meme informations + */ + static protected class ResultMapped { + protected RandomAccessFile raf; + protected int offset; + protected int size; + protected TimeStep step; + protected String name; + protected MatrixND matrix; + + /** read data from file */ + public ResultMapped(RandomAccessFile raf, int offset) throws IOException { + this.raf = raf; + this.offset = offset; + + int stepValue = raf.readInt(); + step = new TimeStep(stepValue); + + name = raf.readUTF(); + + int dimSize = raf.readInt(); + + String[] dimNames = new String[dimSize]; + for (int i=0; i<dimSize; i++) { + dimNames[i] = raf.readUTF(); + } + + int[] dims = new int[dimSize]; + for (int i=0; i<dimSize; i++) { + dims[i] = raf.readInt(); + } + + List[] sems = new List[dimSize]; + for (int i=0; i<dimSize; i++) { + sems[i] = new ArrayList(); + for (int j=0; j<dims[i]; j++) { + String s = raf.readUTF(); + sems[i].add(s); + } + } + + + int size = (int) raf.getFilePointer(); + int dataOffset = offset + size; + + int dataSize = raf.readInt(); + DoubleBigMappedVector data = new DoubleBigMappedVector(raf, dataOffset, dataSize); + this.matrix = matrixFactory.create(name, sems, dimNames, data); + + size += dataSize * 8; /* un double est sur 8 bytes*/ + this.size = size; + } + + /** write date to file */ + public ResultMapped(RandomAccessFile raf, int offset, + TimeStep step, String name, MatrixND matrix) throws IOException { + this.raf = raf; + this.offset = offset; + this.step = step; + this.name = name; + + String[] dimNames = matrix.getDimensionNames(); + int[] dims = matrix.getDim(); + List[] sems = matrix.getSemantics(); + int dataSize = MatrixHelper.getVectorSize(dims); + + raf.write(step.getStep()); // ecriture du pas de temps + raf.writeUTF(name); // ecriture du nom du resultat + raf.write(dims.length); // ecriture de la taille du tableau de dimension et semantique + + for (String s : dimNames) { + raf.writeUTF(s); // ecriture du nom de chaque dimensions + } + for (int d : dims) { + raf.write(d); // ecriture de chaque dimension + } + + // conversion et enregistrement des semantiques + SemanticsDecorator deco = new EntitySemanticsDecorator(); + for (int i=0; i<sems.length; i ++) { + List l = sems[i]; + List undecorate = new ArrayList(l.size()); + sems[i] = undecorate; + for (Object o : l) { + o = deco.undecorate(o); + raf.writeUTF(o.toString()); // ecriture de chaque dimension + } + } + + raf.writeInt(dataSize); + + // on prend la position apres l'ecriture de l'entete + int size = (int) raf.getFilePointer(); + + int dataOffset = offset + size; + // on cree la nouvelle matrice comme il faut (semantique non decore) + DoubleBigMappedVector data = new DoubleBigMappedVector(raf, dataOffset, dataSize); + this.matrix = MatrixFactory.getInstance().create(name, sems, dimNames, data); + // et on met les valeurs de l'ancienne dans la nouvelle + this.matrix.paste(matrix); + + size += dataSize * 8; /* un double est sur 8 bytes*/ + this.size = size; + } + + /** + * retourne la taille en nombre de byte + * @return + */ + public int size() { + return size; + } + + public TimeStep getStep() { + return step; + } + + public String getName() { + return name; + } + + public MatrixND getMatrix() { + return matrix; + } + + public MatrixND getMatrix(TopiaContext tx) { + // on met la matrice dans un decorateur pour convertir automatiquement les semantiques + MatrixND result = new MatrixSemanticsDecorator(matrix, new EntitySemanticsDecorator(tx)); + return result; + } + + } + + /** + * Les ResultStorage ne doivent pas etre instancier directement, mais + * recuperer a partir d'un + * {@link fr.ifremer.isisfish.datastore.SimulationStorage#getResultStorage()} + * + * @param simulation storage to get result + */ + public ResultMappedStorage(SimulationStorage simulation) throws IOException { + this.simulation = simulation; + File file = SimulationStorage.getResultFile(simulation.getDirectory()); + raf = new RandomAccessFile(file, "rw"); + // on lit les donnees deja presente + offset = 0; + while (offset < raf.length()) { + ResultMapped r = new ResultMapped(raf, offset); + storeResult(r); + offset += r.size(); + } + } + + @Override + protected void finalize() throws Throwable { + super.finalize(); + raf.close(); + } + + /** + * Methode interne pour que les deux Map soit mise a jour en meme temps + * C'est la seul methode qui permet d'ajouter des noms de result dans les Map + * @param r + */ + protected void storeResult(ResultMapped r) { + TimeStep step = r.getStep(); + String name = r.getName(); + + getResult(step).put(name, r); + Map<TimeStep, ResultMapped> stepResult = nameStepResults.get(name); + if (stepResult == null) { + stepResult = new TreeMap<TimeStep, ResultMapped>(); + nameStepResults.put(name, stepResult); + } + stepResult.put(step, r); + } + + protected Map<String, ResultMapped> getResult(TimeStep step) { + Map<String, ResultMapped> result = stepNameResults.get(step); + if (result == null) { + result = new TreeMap<String, ResultMapped>(); + stepNameResults.put(step, result); + } + return result; + } + + protected ResultMapped getResult(TimeStep step, String name) { + ResultMapped result = getResult(step).get(name); + return result; + } + + protected ResultMapped getResult(TimeStep step, String name, Population pop) { + name += " " + pop; + ResultMapped result = getResult(step, name); + return result; + } + + protected Map<TimeStep, ResultMapped> getResult(String name, Population pop) { + name += " " + pop; + Map<TimeStep, ResultMapped> result = getResult(name); + return result; + } + + protected Map<TimeStep, ResultMapped> getResult(String name) { + Map<TimeStep, ResultMapped> result = nameStepResults.get(name); + if (result == null) { + // on retourne une map vide, pour ne jamais retourne null + result = Collections.EMPTY_MAP; + } + return result; + } + + + public void addResult(TimeStep step, MatrixND mat) throws IsisFishException { + addResult(false, step, mat.getName(), mat); + } + + public void addResult(TimeStep step, Population pop, MatrixND mat) throws IsisFishException { + addResult(false, step, mat.getName(), pop, mat); + } + + public void addResult(boolean force, TimeStep step, MatrixND mat) throws IsisFishException { + addResult(force, step, mat.getName(), mat); + } + + public void addResult(boolean force, TimeStep step, Population pop, MatrixND mat) throws IsisFishException { + addResult(force, step, mat.getName(), pop, mat); + } + + public void addResult(TimeStep step, String name, Population pop, MatrixND mat) throws IsisFishException { + addResult(false, step, name, pop, mat); + } + + public void addResult(TimeStep step, String name, MatrixND mat) throws IsisFishException { + addResult(false, step, name, mat); + } + + public void addResult(boolean force, TimeStep step, String name, Population pop, MatrixND mat) throws IsisFishException { + if (force || isEnabled(name)) { + doAddResult(step, name + " " + pop, mat); + } + } + + public void addResult(boolean force, TimeStep step, String name, MatrixND mat) throws IsisFishException { + if (force || isEnabled(name)) { + doAddResult(step, name, mat); + } + } + + protected void doAddResult(TimeStep step, String name, MatrixND mat) throws IsisFishException { + // si la matrice n'a pas de semantique on refuse + for (int i = 0; i < mat.getDimCount(); i++) { + // la semantique n'est pas bonne des qu'il y a un null dedans + if (mat.getSemantic(i).contains(null)) { + throw new SimulationException( + "Erreur le résultat que vous souhaitez enregistrer n'a pas d'information convenable pour la dimension: " + + i + " " + mat.getDimensionName(i)); + } + } + + try { + ResultMapped r = new ResultMapped(raf, offset, step, name, mat); + storeResult(r); + offset += r.size(); + } catch (IOException eee) { + log.warn("Can't add result '" + name + "' at step " + step, eee); + } + } + + + + + + + + /** + * Permet de savoir si lorsque l'on ajoutera ce resultat, il sera + * sauvé ou non. + * + * Check for result name returned by : + * <ul> + * <li>{@link Export#getNecessaryResult()}</li> + * <li>{@link SensitivityExport#getNecessaryResult()}</li> + * <li>{@link Rule#getNecessaryResult()}</li> + * <li>{@link SimulationPlan#getNecessaryResult()}</li> + * </ul> + * + * @param name result name + * @return {@code true} if result is enabled + */ + public boolean isEnabled(String name) { + name = name.trim(); + if (enabledResult == null) { + enabledResult = new HashSet<String>(); + + Collection<String> resultEnabled = simulation.getParameter() + .getResultEnabled(); + enabledResult.addAll(resultEnabled); + + // test on export + List<String> exportNames = simulation.getParameter().getExportNames(); + if (exportNames != null) { + for (String exportName : exportNames) { + ExportStorage storage = ExportStorage.getExport(exportName); + try { + Export export = storage.getNewExportInstance(); + for (String resultName : export.getNecessaryResult()) { + enabledResult.add(resultName); + } + } catch (IsisFishException eee) { + if (log.isWarnEnabled()) { + log.warn(_("isisfish.error.instanciate.export", + exportName), eee); + } + } + } + } + + // test on sensitivity export + List<SensitivityExport> sensitivityExports = simulation + .getParameter().getSensitivityExport(); + if (sensitivityExports != null) { + for (SensitivityExport sensitivityExport : sensitivityExports) { + for (String resultName : sensitivityExport.getNecessaryResult()) { + enabledResult.add(resultName); + } + } + } + + // test on rules + List<Rule> rules = simulation.getParameter().getRules(); + if (rules != null) { + for (Rule rule : rules) { + for (String resultName : rule.getNecessaryResult()) { + enabledResult.add(resultName); + } + } + } + + // test on plans + List<SimulationPlan> plans = simulation.getParameter().getSimulationPlans(); + if (plans != null) { + for (SimulationPlan plan : plans) { + for (String resultName : plan.getNecessaryResult()) { + enabledResult.add(resultName); + } + } + } + log.info("Enabled result: " + enabledResult); + } + boolean result = enabledResult.contains(name); + return result; + } + + + public void addActiveRule(TimeStep step, Rule rule) throws IsisFishException { + try { + TopiaContext tx = null; + boolean mustClose = false; + + if (simulation == SimulationContext.get().getSimulationStorage()) { + tx = SimulationContext.get().getDbResult(); + } + if (tx == null) { + // not in simulation, create transaction + tx = simulation.getStorage().beginTransaction(); + mustClose = true; + } + ActiveRuleDAO ps = IsisFishDAOHelper.getActiveRuleDAO(tx); + ActiveRule result = ps.create(); + result.setActiveRuleStep(step); + result.setName(RuleStorage.getName(rule)); + result.setParam(RuleStorage.getParamAsString(rule)); + ps.update(result); + if (mustClose) { + tx.commitTransaction(); + tx.closeContext(); + } + } catch (TopiaException eee) { + throw new IsisFishException("Can't add result", eee); + } + } + + /** + * Retourne la liste de tous les résultats. Si le résultat est categorisé + * par une population alors le nom de la population est automatiquement + * ajouté au nom du résultat. + */ + public List<String> getResultName() { + List<String> result = new ArrayList<String>(nameStepResults.keySet()); + return result; + } + + /** + * Retourne la matrice stocke pour un pas de temps + * @param step le pas de temps que l'on souhaite + * @param pop la population pour lequelle on souhaite le resultat + * @param name le nom des resultats dont on veut la matrice + * @return La matrice demandée ou null si aucune matrice ne correspond a + * la demande. + */ + public MatrixND getMatrix(TimeStep step, Population pop, String name) { + String newName = name + " " + pop; + return getMatrix(step, newName, null); + } + + public MatrixND getMatrix(TimeStep step, String name) { + return getMatrix(step, name, null); + } + + /** + * Retourne une matrice contenant tous les pas de temps. + * + * @param name le nom des resultats dont on veut une matrice globale. + */ + public MatrixND getMatrix(TimeStep step, String name, TopiaContext tx) { + ResultMapped r = getResult(step, name); + MatrixND mat = null; + if (r != null) { + mat = r.getMatrix(tx); + } + return mat; + } + + /** + * Retourne une matrice contenant tous les pas de temps. + * @param pop la population pour lequel on souhaite la matrice + * @param name le nom des resultats dont on veut une matrice globale. + */ + public MatrixND getMatrix(Population pop, String name) { + String newName = name + " " + pop; + return getMatrix(newName, null); + } + + /** + * Retourne une matrice contenant tous les pas de temps. + * + * @param name le nom des resultats dont on veut une matrice globale. + */ + public MatrixND getMatrix(String name) { + return getMatrix(name, null); + } + + /** + * Retourne une matrice contenant tous les pas de temps. + * @param name le nom des resultats dont on veut une matrice globale. + */ + public MatrixND getMatrix(String name, TopiaContext tx) { + log.debug("Get result: " + name); + + MatrixND resultMat = null; + Map<TimeStep, ResultMapped> results = getResult(name); + // recuperation des resultats qui nous interesse + if (!results.isEmpty()) { + // creation de la liste de date + TimeStep lastStep = getLastStep(); + List<TimeStep> steps = new ArrayList<TimeStep>(); + TimeStep step = new TimeStep(0); + steps.add(step); + while (step.before(lastStep)) { + step = step.next(); + steps.add(step); + } + + if (log.isTraceEnabled()) { + log.trace("Steps list : " + steps); + } + + + MatrixND mat = results.values().iterator().next().getMatrix(); + + // recuperation des noms des dimensions + String[] dimNames = new String[1 + mat.getDimCount()]; + dimNames[0] = _("isisfish.common.date"); + for (int i = 1; i < dimNames.length; i++) { + dimNames[i] = mat.getDimensionName(i - 1); + } + + // creation de la semantique pour la matrice resultat. +1 pour les dates + List[] sem = new List[1 + mat.getDimCount()]; + sem[0] = steps; + + for (int i = 1; i < sem.length; i++) { + sem[i] = new HashList(); + } + + for (ResultMapped result : results.values()) { + MatrixND mattmp = result.getMatrix(); + if (log.isTraceEnabled()) { + log.trace("Ajout de la semantics: " + + Arrays.asList(mattmp.getSemantics())); + } + + for (int s = 0; s < mattmp.getDimCount(); s++) { + sem[s + 1].addAll(mattmp.getSemantic(s)); + } + } + + if (log.isTraceEnabled()) { + log.trace("La semantique final est: " + Arrays.asList(sem)); + } + + // creation de la matrice resultat + resultMat = matrixFactory.create(name, sem, dimNames); + + // recuperation du resultat pour chaque date de la simulation, de Date(0) à lastDate + for (ResultMapped result : results.values()) { + TimeStep d = result.getStep(); + mat = result.getMatrix(); + // on met ce resultat dans la matrice result si besoin + if (mat != null) { + // on recupere dans la matrice resultat l'endroit on il faut + // mettre la matrice + MatrixND submat = resultMat.getSubMatrix(0, d, 1); + // on met les valeur de mat dans la sous matrice extraite + for (MatrixIterator mi = mat.iterator(); mi.next();) { + submat.setValue( + ArrayUtil.concat(new Object[] { d }, + mi.getSemanticsCoordinates()), mi.getValue()); + } + } + } + } + if (resultMat != null) { + // on decore la matrice resultat au dernier moment, tous les calcules + // ce font avec les strings + resultMat = new MatrixSemanticsDecorator(resultMat, new EntitySemanticsDecorator(tx)); + } + return resultMat; + } + + /** + * Get last simulation date. + * + * @return last simulation date + */ + public TimeStep getLastStep() { + int monthNumber = simulation.getParameter().getNumberOfYear() + * Month.NUMBER_OF_MONTH; + TimeStep result = new TimeStep(monthNumber - 1); // -1 because date begin at 0 + return result; + } + + /* + * @see fr.ifremer.isisfish.simulator.SimulationResultListener#addResult(fr.ifremer.isisfish.simulator.SimulationContext, fr.ifremer.isisfish.types.TimeStep, java.lang.String, org.nuiton.math.matrix.MatrixND) + */ + @Override + public void addResult(SimulationContext context, TimeStep step, String name, + MatrixND mat) throws IsisFishException { + doAddResult(step, name, mat); + } + + /* + * @see fr.ifremer.isisfish.simulator.SimulationResultGetter#getMatrix(fr.ifremer.isisfish.simulator.SimulationContext, fr.ifremer.isisfish.types.TimeStep, java.lang.String) + */ + @Override + public MatrixND getMatrix(SimulationContext context, TimeStep step, String name) { + MatrixND result = null; + try { + result = getMatrix(step, name, context.getDB()); + } catch (TopiaException eee) { + if (log.isWarnEnabled()) { + log.warn(String.format("Can't get result: %1$s", name), eee); + } + } + return result; + + } + + /* + * @see fr.ifremer.isisfish.simulator.SimulationResultGetter#getMatrix(fr.ifremer.isisfish.simulator.SimulationContext, java.lang.String) + */ + @Override + public MatrixND getMatrix(SimulationContext context, String name) { + MatrixND result = null; + try { + result = getMatrix(name, context.getDB()); + } catch (TopiaException eee) { + if (log.isWarnEnabled()) { + log.warn(String.format("Can't get result: %1$s", name), eee); + } + } + return result; + } + + /* + * @see fr.ifremer.isisfish.simulator.SimulationListener#afterSimulation(fr.ifremer.isisfish.simulator.SimulationContext) + */ + @Override + public void afterSimulation(SimulationContext context) { + } + + /* + * @see fr.ifremer.isisfish.simulator.SimulationListener#beforeSimulation(fr.ifremer.isisfish.simulator.SimulationContext) + */ + @Override + public void beforeSimulation(SimulationContext context) { + } + + // public void addActivatedRule(ResultStorage self, Date date, RegleParam rule){ + // List rules = (List)activatedRules.get(date); + // if(rules == null){ + // activatedRules.put(date, rules = new LinkedList()); + // } + // rules.add(rule); + // } + + // /** + // * Retourne pour une date données tous les RegleParam qui ont été activé + // * a la date demandé. + // * @return une list de {@link fr.ifremer.nodb.RegleParam} + // */ + // public List getActivatedRule(ResultStorage self, Date date){ + // List rules = (List)activatedRules.get(date); + // if(rules == null){ + // activatedRules.put(date, rules = new LinkedList()); + // } + // return rules; + // } + +} \ No newline at end of file Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java 2012-08-30 14:46:24 UTC (rev 3749) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java 2012-08-31 13:09:22 UTC (rev 3750) @@ -74,6 +74,7 @@ public static final String CONTROL_FILENAME = "control"; public static final String PARAMETERS_FILENAME = "parameters.properties"; public static final String RESULT_XML_FILENAME = "isis-mexico-output.xml"; + public static final String RESULT_FILENAME = "results.mapped"; public static final String RESULT_EXPORT_DIRECTORY = "resultExports"; public static final String DESIGN_PLAN_FILENAME = "isis-mexico-designplan.xml"; public static final String SENSITIVITY_RESULTS = "sensitivityresults"; @@ -183,7 +184,7 @@ /** * Retourne le fichier de stockage des inforations de la simulation. - * + * * @param root le repertoire de stockage de la simulation * @return information file */ @@ -195,7 +196,7 @@ /** * Retourne le fichier de stockage des resultats sous format XML mexico * de la simulation. - * + * * @param root le repertoire de stockage de la simulation * @return mexico xml file */ @@ -205,6 +206,18 @@ } /** + * Retourne le fichier de stockage des resultats + * de la simulation. + * + * @param root le repertoire de stockage de la simulation + * @return + */ + public static File getResultFile(File root) { + File result = new File(root, RESULT_FILENAME); + return result; + } + + /** * Retourne le fichier de stockage des parametres de la simulation courante. * * @return parameter file @@ -437,6 +450,8 @@ */ public ResultStorage getResultStorage() { if (resultStorage == null) { + // FIXME poussin 20120831 en fonction de la version de la base + // instancier un ResultStorage ou un ResultMappedStorage resultStorage = new ResultStorage(this); } return resultStorage;

1 0

r3749 - trunk
by tchemit＠users.forge.codelutin.com 30 Aug '12

30 Aug '12

Author: tchemit Date: 2012-08-30 16:46:24 +0200 (Thu, 30 Aug 2012) New Revision: 3749 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3749 Log: Update mavenpom4redmine to 3.3.7. Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-08-30 14:07:12 UTC (rev 3748) +++ trunk/pom.xml 2012-08-30 14:46:24 UTC (rev 3749) @@ -6,7 +6,7 @@ <parent> <groupId>org.nuiton</groupId> <artifactId>mavenpom4redmine</artifactId> - <version>3.3.6</version> + <version>3.3.7</version> </parent> <groupId>fr.ifremer</groupId>

1 0

r3748 - in trunk/src: main/java/fr/ifremer/isisfish main/java/fr/ifremer/isisfish/simulator/launcher main/java/fr/ifremer/isisfish/ui main/java/fr/ifremer/isisfish/ui/config main/resources/i18n main/resources/templates/ssh test/java/fr/ifremer/isisfish/simulator/launcher
by echatellier＠users.forge.codelutin.com 30 Aug '12

30 Aug '12

Author: echatellier Date: 2012-08-30 16:07:12 +0200 (Thu, 30 Aug 2012) New Revision: 3748 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3748 Log: fixes #1442: Add option to control subprocess allocated memory fixes #1443: Add option to control caparmor process allocated memory fixes #1445: Add option to control subprocess max simultaneous process count Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SubProcessSimulationLauncher.java trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigAction.java trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigUI.jaxx trunk/src/main/resources/i18n/isis-fish_en_GB.properties trunk/src/main/resources/i18n/isis-fish_fr_FR.properties trunk/src/main/resources/templates/ssh/qsub-script.ftl trunk/src/test/java/fr/ifremer/isisfish/simulator/launcher/SshSimulatorLauncherTest.java Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2012-08-30 13:50:52 UTC (rev 3747) +++ trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2012-08-30 14:07:12 UTC (rev 3748) @@ -386,6 +386,36 @@ } /** + * Retourne le nombre maximum de thread à utiliser en in process. + * + * @return number of thread to use + */ + public int getSimulatorInMaxThreads() { + int result = getOptionAsInt(Option.SIMULATOR_IN_MAXTHREADS.key); + return result; + } + + /** + * Retourne le nombre de sous processus maximum a creer. + * + * @return number of sub process to create + */ + public int getSimulatorSubMaxProcess() { + int result = getOptionAsInt(Option.SIMULATOR_SUB_MAXPROCESS.key); + return result; + } + + /** + * Retourne la quantité de ram (Xmx) a alloue au sous processus. + * + * @return memory amount to use for sub process + */ + public String getSimulatorSubMaxMemory() { + String result = getOption(Option.SIMULATOR_SUB_MAXMEMORY.key); + return result; + } + + /** * Retourne l'url du serveur de simulation accessible via SSH. * * @return simulator server @@ -601,6 +631,25 @@ } /** + * Retourne la quantité de ram (Xmx) a alloue au processus sur caparmor. + * + * @return number of thread to use + */ + public String getSimulatorSshMaxMemory() { + String result = getOption(Option.SIMULATOR_SSH_MAXMEMORY.key); + return result; + } + + /** + * Set ssh simulation process memory to use + * + * @param memory memory + */ + public void setSimulatorSshMaxMemory(String memory) { + setOption(Option.SIMULATOR_SSH_MAXMEMORY.key, memory); + } + + /** * Retourne la clé privée de l'utilisteur courant. * * @return private ssh key path @@ -911,6 +960,14 @@ SIMULATOR_LAUNCHER2(SimulationService.SIMULATION_LAUNCHER + ".1", n_("isisfish.config.main.subSimulator.description"), SubProcessSimulationLauncher.class.getName()), SIMULATOR_LAUNCHER_REMOTE(SimulationService.SIMULATION_LAUNCHER + ".2", n_("isisfish.config.main.remoteCaparmor.description"), SSHSimulatorLauncher.class.getName()), + /** Nombre maximum de thread de simulation in process. */ + SIMULATOR_IN_MAXTHREADS("simulation.in.max.threads", n_("isisfish.config.main.simulation.in.max.threads.description"), "1"), + + /** Nombre max de sous processus à lancer (-1 = pas de limite). */ + SIMULATOR_SUB_MAXPROCESS("simulation.sub.max.process", n_("isisfish.config.main.simulation.sub.max.process.description"), "-1"), + /** Mémoire max (Xmx) allouée aux sous processus. */ + SIMULATOR_SUB_MAXMEMORY("simulation.sub.max.memory", n_("isisfish.config.main.simulation.sub.max.memory.description"), "1024M"), + /** Serveur accessible par ssh : address */ SIMULATOR_SSH_SERVER("simulation.ssh.server", n_("isisfish.config.main.simulation.ssh.server.description"), "caparmor-sftp"), /** Serveur accessible par ssh : login */ @@ -933,6 +990,8 @@ SIMULATOR_SSH_CONTROLCHECKINTERVAL("simulation.ssh.control.check.interval", n_("isisfish.config.main.simulation.ssh.control.check.interval.description"), "120"), /** Serveur accessible par SSH : nombre de thread au maximum a utilise simultanement */ SIMULATOR_SSH_MAXTHREADS("simulation.ssh.max.threads", n_("isisfish.config.main.simulation.ssh.max.threads.description"), "1"), + /** Serveur accessible par SSH : mémoire (Xmx) allouée pour les process java sur caparmor */ + SIMULATOR_SSH_MAXMEMORY("simulation.ssh.max.memory", n_("isisfish.config.main.simulation.ssh.max.memory.description"), "2000M"), /** Application locale (for i18n init). */ LOCALE("locale", n_("isisfish.config.main.locale.description"), "fr_FR"), Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2012-08-30 13:50:52 UTC (rev 3747) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2012-08-30 14:07:12 UTC (rev 3748) @@ -171,7 +171,7 @@ * @see fr.ifremer.isisfish.simulator.launcher.SimulatorLauncher#maxSimulationThread() */ public int maxSimulationThread() { - return 1; + return IsisFish.config.getSimulatorInMaxThreads(); } /* @@ -181,7 +181,6 @@ public int getCheckProgressionInterval() { // par defaut, pour les in process 5 secondes - int interval = 1; return interval; } Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java 2012-08-30 13:50:52 UTC (rev 3747) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java 2012-08-30 14:07:12 UTC (rev 3748) @@ -176,7 +176,7 @@ @Override public int maxSimulationThread() { - // met le serveur les lance quand il veut + // mais le serveur les lance quand il veut int maxSimulationThread = IsisFish.config.getSimulatorSshMaxThreads(); if (maxSimulationThread <= 0) { @@ -1104,6 +1104,7 @@ root.put("isishome", IsisFish.config.getSimulatorSshIsisHome()); root.put("isistemp", getRemoteTempDirectory()); root.put("javapath", IsisFish.config.getSimulatorSshJavaPath()); + root.put("javamemory", IsisFish.config.getSimulatorSshMaxMemory()); root.put("simulationid", simuationId); root.put("simulationzip", simulationZip); root.put("simulationstandalonezip", standaloneZip); Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SubProcessSimulationLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SubProcessSimulationLauncher.java 2012-08-30 13:50:52 UTC (rev 3747) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SubProcessSimulationLauncher.java 2012-08-30 14:07:12 UTC (rev 3748) @@ -43,6 +43,8 @@ import org.apache.commons.logging.LogFactory; import org.nuiton.util.FileUtil; +import com.sun.tools.internal.jxc.gen.config.Config; + import fr.ifremer.isisfish.IsisFish; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.simulator.SimulationControl; @@ -110,8 +112,15 @@ @Override public int maxSimulationThread() { - // TODO rendre configurable le nombre de processeurs a utiliser - int result = Runtime.getRuntime().availableProcessors(); + + int result = IsisFish.config.getSimulatorSubMaxProcess(); + + // s'il n'y a pas de configuration utilisateur particulière + // on utilise le nombre de processeur physique + if (result <= 0) { + result = Runtime.getRuntime().availableProcessors(); + } + return result; } @@ -189,7 +198,7 @@ // common args List<String> command = new ArrayList<String>(); command.add(java); - command.add("-Xmx2048M"); + command.add("-Xmx" + IsisFish.config.getSimulatorSubMaxMemory()); // jri args String libraryPath = System.getProperty("java.library.path"); Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java 2012-08-30 13:50:52 UTC (rev 3747) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java 2012-08-30 14:07:12 UTC (rev 3748) @@ -222,6 +222,12 @@ modelBuilder.addOption(IsisConfig.Option.SIMULATION_SHOW_ONLY_ERROR); modelBuilder.addOption(IsisConfig.Option.SIMULATION_SCRIPT_AUTOCONFIG); + // category simulation + modelBuilder.addCategory(_("isisfish.config.category.simulation"), _("isisfish.config.category.simulation.description")); + modelBuilder.addOption(IsisConfig.Option.SIMULATOR_IN_MAXTHREADS); + modelBuilder.addOption(IsisConfig.Option.SIMULATOR_SUB_MAXPROCESS); + modelBuilder.addOption(IsisConfig.Option.SIMULATOR_SUB_MAXMEMORY); + // category database vcs modelBuilder.addCategory(_("isisfish.config.category.officialvcs"), _("isisfish.config.category.officialvcs.description")); modelBuilder.addOption(IsisConfig.Option.VCS_TYPE); Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigAction.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigAction.java 2012-08-30 13:50:52 UTC (rev 3747) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigAction.java 2012-08-30 14:07:12 UTC (rev 3748) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2009 - 2011 Ifremer, Code Lutin, Chatellier Eric + * Copyright (C) 2009 - 2012 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 @@ -79,6 +79,7 @@ protected String currentSSHPbsBinPath; protected String currentSSHPbsQsubOptions; protected String currentSSHMaxThreads; + protected String currentSSHMaxMemory; protected String currentSSHControlInterval; /** @@ -109,6 +110,7 @@ configUI.getSshPbsQsubOptionsField().setText(IsisFish.config.getSimulatorSshPbsQsubOptions()); configUI.getSshControlIntervalField().setText(String.valueOf(IsisFish.config.getSimulatorSshControlCheckInterval())); configUI.getSshMaxThreadsField().setText(String.valueOf(IsisFish.config.getSimulatorSshMaxThreads())); + configUI.getSshMaxMemoryField().setText(IsisFish.config.getSimulatorSshMaxMemory()); doCheck(); } @@ -207,6 +209,9 @@ } else { setColor(false, configUI.getSshMaxThreadsField()); } + + // currentSSHMaxMemory + currentSSHMaxMemory = configUI.getSshMaxMemoryField().getText().trim(); // currentSSHControlInterval currentSSHControlInterval = configUI.getSshControlIntervalField() @@ -236,6 +241,7 @@ IsisFish.config.setSimulatorSshPbsQsubOptions(currentSSHPbsQsubOptions); IsisFish.config.setSimulatorSshControlCheckInterval(Integer.parseInt(currentSSHControlInterval)); IsisFish.config.setSimulatorSshMaxThreads(Integer.parseInt(currentSSHMaxThreads)); + IsisFish.config.setSimulatorSshMaxMemory(currentSSHMaxMemory); IsisFish.config.saveForUser(); configUI.dispose(); Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigUI.jaxx =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigUI.jaxx 2012-08-30 13:50:52 UTC (rev 3747) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigUI.jaxx 2012-08-30 14:07:12 UTC (rev 3748) @@ -5,7 +5,7 @@ $Id$ $HeadURL$ %% - Copyright (C) 2009 - 2011 Ifremer, CodeLutin, Chatellier Eric + Copyright (C) 2009 - 2012 Ifremer, CodeLutin, Chatellier Eric %% This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as @@ -157,6 +157,17 @@ </row> <row fill='horizontal'> <cell> + <JLabel id='sshMaxMemoryLabel' text='isisfish.config.main.simulation.ssh.max.memory' + toolTipText='isisfish.config.main.simulation.ssh.max.memory.description' /> + </cell> + <cell> + <JTextField id='sshMaxMemoryField' + toolTipText='isisfish.config.main.simulation.ssh.max.memory.description' + onKeyReleased="getAction().doCheck()" /> + </cell> + </row> + <row fill='horizontal'> + <cell> <JLabel id='sshControlIntervalLabel' text='isisfish.config.main.simulation.ssh.control.check.interval' toolTipText='isisfish.config.main.simulation.ssh.control.check.interval.description' /> </cell> Modified: trunk/src/main/resources/i18n/isis-fish_en_GB.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2012-08-30 13:50:52 UTC (rev 3747) +++ trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2012-08-30 14:07:12 UTC (rev 3748) @@ -145,6 +145,8 @@ isisfish.config.category.misc.description=Miscealenous isisfish.config.category.officialvcs=Official VCS isisfish.config.category.officialvcs.description=Official VCS repository +isisfish.config.category.simulation=Simulations +isisfish.config.category.simulation.description=Simulation execution configuration isisfish.config.database.lockmode.description=Database lock mode isisfish.config.main.compileDirectory.description=Script compilation directory isisfish.config.main.configFileName.description=Configuration filename @@ -166,6 +168,7 @@ isisfish.config.main.performvcsupdate.description=Perform vcs update isisfish.config.main.remoteCaparmor.description=Remote simulator launcher name isisfish.config.main.script.autoconfig.description=Display a dialog to force script configuration +isisfish.config.main.simulation.in.max.threads.description=Max threads count in current process isisfish.config.main.simulation.ssh.control.check.interval=Control check interval (seconds) isisfish.config.main.simulation.ssh.control.check.interval.description=Control check interval (seconds) isisfish.config.main.simulation.ssh.datapath=ISIS-Fish database @@ -174,6 +177,8 @@ isisfish.config.main.simulation.ssh.isis.home.description=ISIS-Fish installation directory isisfish.config.main.simulation.ssh.javapath=Java path isisfish.config.main.simulation.ssh.javapath.description=Java location on remote server (full path or relative to $PATH, by default value is caparmor configuration) +isisfish.config.main.simulation.ssh.max.memory=Ssh simulation Xmx allocated memory +isisfish.config.main.simulation.ssh.max.memory.description=Ssh simulation Xmx allocated memory isisfish.config.main.simulation.ssh.max.threads=SSH threads count isisfish.config.main.simulation.ssh.max.threads.description=Number of simultaneous simulations to do through SSH. Might only be usefull for dependent analysis plans. Otherwise keep value at '1'. isisfish.config.main.simulation.ssh.pbsbinpath=PBS executables directory @@ -188,6 +193,8 @@ isisfish.config.main.simulation.ssh.userhome.description=User home directory isisfish.config.main.simulation.ssh.username=SSH identifier isisfish.config.main.simulation.ssh.username.description=SSH identifier +isisfish.config.main.simulation.sub.max.memory.description=Sub process simulation Xmx allocated memory +isisfish.config.main.simulation.sub.max.process.description=Max sub process count (using -1 value will use available processor count) isisfish.config.main.simulationShowOnlyError.description= isisfish.config.main.smtpServer.description=Smtp server address isisfish.config.main.subSimulator.description=Sub process simulator launcher name Modified: trunk/src/main/resources/i18n/isis-fish_fr_FR.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2012-08-30 13:50:52 UTC (rev 3747) +++ trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2012-08-30 14:07:12 UTC (rev 3748) @@ -145,6 +145,8 @@ isisfish.config.category.misc.description=Divers isisfish.config.category.officialvcs=VCS Officiel isisfish.config.category.officialvcs.description=Dépôt contenant les scripts officiels +isisfish.config.category.simulation=Simulations +isisfish.config.category.simulation.description=Configuration des simulations isisfish.config.database.lockmode.description=Méthode de vérouillage à utiliser pour la base de données isisfish.config.main.compileDirectory.description=le répertoire où sont compilés les scripts isisfish.config.main.configFileName.description=le fichier de configuration à utiliser @@ -166,6 +168,7 @@ isisfish.config.main.performvcsupdate.description=Met à jour le dépôt VCS isisfish.config.main.remoteCaparmor.description=Nom du lanceur de simulation distante isisfish.config.main.script.autoconfig.description=Affiche une fenêtre pour forcer la configuration des scripts +isisfish.config.main.simulation.in.max.threads.description=Nombre de thread maximum dans le processus courant isisfish.config.main.simulation.ssh.control.check.interval=Vérification de la progression (secondes) isisfish.config.main.simulation.ssh.control.check.interval.description=Temps d'attente en secondes entre deux vérifications de progression isisfish.config.main.simulation.ssh.datapath=Base de données @@ -174,6 +177,8 @@ isisfish.config.main.simulation.ssh.isis.home.description=Emplacement d'installation d'ISIS-Fish sur le serveur isisfish.config.main.simulation.ssh.javapath=Emplacement de java isisfish.config.main.simulation.ssh.javapath.description=Emplacement de java sur le serveur (chemin total, ou relatif au $PATH, par défaut la valeur est celle de caparmor) +isisfish.config.main.simulation.ssh.max.memory=Quantité de mémoire allouée +isisfish.config.main.simulation.ssh.max.memory.description=Quantité de mémoire maximum allouée (Xmx) isisfish.config.main.simulation.ssh.max.threads=Nombre de thread SSH isisfish.config.main.simulation.ssh.max.threads.description=Nombre de simulation simultanée à faire en SSH. Attention, ne doit être utilisé que pour faire plusieurs plans de simulation dépendants en même temps, sinon laisser '1'. isisfish.config.main.simulation.ssh.pbsbinpath=Emplacement des executables PBS @@ -188,6 +193,8 @@ isisfish.config.main.simulation.ssh.userhome.description=Répertoire d'accueil de l'utilisateur isisfish.config.main.simulation.ssh.username=Identifiant isisfish.config.main.simulation.ssh.username.description=Identifiant SSH pour se connecter au serveur +isisfish.config.main.simulation.sub.max.memory.description=Quantité de mémoire maximum allouée au sous processus +isisfish.config.main.simulation.sub.max.process.description=Nombre maximum de sous processus (une valeur de -1 utilisera le nombre de processeur disponible) isisfish.config.main.simulationShowOnlyError.description=pour indiquer si l'on doit conserver dans l'UI des simulations terminées uniquement celles avec erreur isisfish.config.main.smtpServer.description=le nom du serveur smtp à utiliser pour envoyer les courriels isisfish.config.main.subSimulator.description=Nom du simulateur en sous processus Modified: trunk/src/main/resources/templates/ssh/qsub-script.ftl =================================================================== --- trunk/src/main/resources/templates/ssh/qsub-script.ftl 2012-08-30 13:50:52 UTC (rev 3747) +++ trunk/src/main/resources/templates/ssh/qsub-script.ftl 2012-08-30 14:07:12 UTC (rev 3748) @@ -29,7 +29,7 @@ setenv R_HOME /appli/R/2.15.0-gnu-4.3/lib64/R setenv LD_LIBRARY_PATH ${r"${R_HOME}"}/lib -<#assign commonCommand="${javapath} -Djava.library.path=jri64 -DR.type=jni -Xmx2000M -jar isis-fish*.jar" /> +<#assign commonCommand="${javapath} -Djava.library.path=jri64 -DR.type=jni -Xmx${javamemory} -jar isis-fish*.jar" /> <#assign commonOptions="--option launch.ui false --option perform.vcsupdate false --option perform.migration false --option perform.cron false" /> <#if qsubmutiplejob> <#-- localsimulationid is short simulation id version --> Modified: trunk/src/test/java/fr/ifremer/isisfish/simulator/launcher/SshSimulatorLauncherTest.java =================================================================== --- trunk/src/test/java/fr/ifremer/isisfish/simulator/launcher/SshSimulatorLauncherTest.java 2012-08-30 13:50:52 UTC (rev 3747) +++ trunk/src/test/java/fr/ifremer/isisfish/simulator/launcher/SshSimulatorLauncherTest.java 2012-08-30 14:07:12 UTC (rev 3748) @@ -329,4 +329,20 @@ Assert.assertTrue(content.contains("${R_HOME}/lib")); } + + /** + * Test que memoire définie dans la configuration est bien présente. + * + * @throws IOException + * @throws TemplateException + */ + @Test + public void testFreemarkerTemplateMemory() throws IOException, TemplateException { + SSHSimulatorLauncher launcher = new SSHSimulatorLauncher(); + String content = launcher.getSimulationScriptLaunchContent( + SSHSimulatorLauncher.QSUB_SCRIPT_TEMPLATE, "", + "", true, "", "", true); + + Assert.assertTrue(content.contains("Xmx2000M")); + } } \ No newline at end of file

1 0

r3747 - trunk/src/main/java/fr/ifremer/isisfish/util
by echatellier＠users.forge.codelutin.com 30 Aug '12

30 Aug '12

Author: echatellier Date: 2012-08-30 15:50:52 +0200 (Thu, 30 Aug 2012) New Revision: 3747 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3747 Log: Wrong import Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisMatrixSemanticMapper.java Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisMatrixSemanticMapper.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisMatrixSemanticMapper.java 2012-08-30 13:45:31 UTC (rev 3746) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisMatrixSemanticMapper.java 2012-08-30 13:50:52 UTC (rev 3747) @@ -35,7 +35,6 @@ import fr.ifremer.isisfish.entities.PopulationDAO; import fr.ifremer.isisfish.entities.PopulationGroup; import fr.ifremer.isisfish.entities.PopulationGroupDAO; -import fr.ifremer.isisfish.entities.Result; import fr.ifremer.isisfish.simulator.SimulationContext; /**

1 0

r3746 - in trunk/src: main/java/fr/ifremer/isisfish/util test/java/fr/ifremer/isisfish/util
by echatellier＠users.forge.codelutin.com 30 Aug '12

30 Aug '12

Author: echatellier Date: 2012-08-30 15:45:31 +0200 (Thu, 30 Aug 2012) New Revision: 3746 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3746 Log: fixes #1444: Fix matrix import semantic mapper for PopulationGroup Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisMatrixSemanticMapper.java trunk/src/test/java/fr/ifremer/isisfish/util/IsisMatrixSemanticMapperTest.java Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisMatrixSemanticMapper.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisMatrixSemanticMapper.java 2012-08-30 12:45:25 UTC (rev 3745) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisMatrixSemanticMapper.java 2012-08-30 13:45:31 UTC (rev 3746) @@ -31,6 +31,11 @@ import org.nuiton.topia.persistence.TopiaEntity; import fr.ifremer.isisfish.IsisFishDAOHelper; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.entities.PopulationDAO; +import fr.ifremer.isisfish.entities.PopulationGroup; +import fr.ifremer.isisfish.entities.PopulationGroupDAO; +import fr.ifremer.isisfish.entities.Result; import fr.ifremer.isisfish.simulator.SimulationContext; /** @@ -90,7 +95,30 @@ // In simulation context : Object value = null; try { - if (TopiaEntity.class.isAssignableFrom(type)) { + // les populations groupes sont speciaux car ils n'ont pas de + // noms. Dans l'import il sont composé du nom de la population + // et du numero de groupe séparé par +. + if (PopulationGroup.class.isAssignableFrom(type)) { + int separatorIndex = valueId.indexOf('+'); + if (separatorIndex >= 0) { + String popName = valueId.substring(0, separatorIndex); + int groupId = Integer.parseInt(valueId.substring(separatorIndex + 1)); + + TopiaContext context = SimulationContext.get().getDB(); + PopulationDAO populationDao = IsisFishDAOHelper.getPopulationDAO(context); + PopulationGroupDAO populationGroupDAO = IsisFishDAOHelper.getPopulationGroupDAO(context); + Population population = populationDao.findByName(popName); + value = populationGroupDAO.findByProperties( + PopulationGroup.PROPERTY_POPULATION, population, + PopulationGroup.PROPERTY_ID, groupId); + } else { + if (log.isWarnEnabled()) { + log.warn("PopulationGroup identifiant doesn't contains '+' separator"); + } + value = valueId; + } + } + else if (TopiaEntity.class.isAssignableFrom(type)) { TopiaContext context = SimulationContext.get().getDB(); TopiaDAO dao = IsisFishDAOHelper.getDAO(context, type); value = dao.findByProperty("name", valueId); Modified: trunk/src/test/java/fr/ifremer/isisfish/util/IsisMatrixSemanticMapperTest.java =================================================================== --- trunk/src/test/java/fr/ifremer/isisfish/util/IsisMatrixSemanticMapperTest.java 2012-08-30 12:45:25 UTC (rev 3745) +++ trunk/src/test/java/fr/ifremer/isisfish/util/IsisMatrixSemanticMapperTest.java 2012-08-30 13:45:31 UTC (rev 3746) @@ -45,6 +45,7 @@ import fr.ifremer.isisfish.AbstractIsisFishTest; import fr.ifremer.isisfish.IsisFishDAOHelper; import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; import fr.ifremer.isisfish.simulator.SimulationContext; import fr.ifremer.isisfish.types.TimeStep; @@ -149,4 +150,31 @@ Assert.assertEquals(2.0, m.getValue(0, 0, 0), 0.001); Assert.assertEquals(1.0, m.getValue(0, 0, 1), 0.001); } + + /** + * Test la conversion des entités. + * @throws IOException + * @throws TopiaException + */ + @Test + public void testImportPopulationGroup() throws IOException, TopiaException { + String data = "[1, 3, 1]\n" + + "Population:test population\n" + + "PopulationGroup:test population+2,test population+1,test population+0\n" + + "Zone:Zone test1\n" + + "0;2;0;42.0"; + + TopiaContext tx = SimulationContext.get().getDB(); + + Population pop = IsisFishDAOHelper.getPopulationDAO(tx).findByName("test population"); + List[] sems = new List[] { + Collections.singletonList(pop), + Arrays.asList(pop.getPopulationGroup().get(0), pop.getPopulationGroup().get(1), pop.getPopulationGroup().get(2)), + Collections.singletonList(IsisFishDAOHelper.getZoneDAO(tx).findByName("Zone test1")), + }; + MatrixND m = MatrixFactory.getInstance().create(sems); + m.importCSV(new StringReader(data), null); + + Assert.assertEquals(42.0, m.getValue(0, 0, 0), 0.001); + } }

1 0

r3745 - in trunk/src/main: java/fr/ifremer/isisfish java/fr/ifremer/isisfish/datastore java/fr/ifremer/isisfish/simulator java/fr/ifremer/isisfish/simulator/launcher resources/i18n
by echatellier＠users.forge.codelutin.com 30 Aug '12

30 Aug '12

Author: echatellier Date: 2012-08-30 14:45:25 +0200 (Thu, 30 Aug 2012) New Revision: 3745 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3745 Log: fixes #1435 : Memory leak is still present when reading result during export Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationExportResultWrapper.java trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SubProcessSimulationLauncher.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 2012-08-27 19:41:06 UTC (rev 3744) +++ trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2012-08-30 12:45:25 UTC (rev 3745) @@ -119,7 +119,7 @@ * migration de donnees demande automatiquement un changement de version * d'application. */ - protected final static Version version = new Version(4, 1, 1, 0); + protected final static Version version = new Version(4, 1, 1, 1); protected final static Version majorVersion = new Version(version.getNumber(0)); protected final static Version databaseVersion = new Version( Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java 2012-08-27 19:41:06 UTC (rev 3744) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java 2012-08-30 12:45:25 UTC (rev 3745) @@ -37,11 +37,13 @@ import org.apache.commons.collections.map.ReferenceMap; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +import org.hibernate.HibernateException; import org.nuiton.math.matrix.MatrixFactory; import org.nuiton.math.matrix.MatrixIterator; import org.nuiton.math.matrix.MatrixND; import org.nuiton.topia.TopiaContext; import org.nuiton.topia.TopiaException; +import org.nuiton.topia.framework.TopiaContextImpl; import org.nuiton.util.ArrayUtil; import org.nuiton.util.HashList; @@ -357,6 +359,9 @@ } // on fait une copie pour avoir reellement des resultats independant + // FIXME echatellier 20120829 : faire une copie optimiser + // suivant l'implementation du vector plutot qu'un parcourt + // via un iterateur de semantiques (plus couteux) MatrixND newMat = mat.copy(); try { ResultDAO resultPS = IsisFishDAOHelper.getResultDAO(tx); @@ -489,6 +494,11 @@ // donc mettre la matrice et la connexion dans une map // la matrice dans une weak reference. Des que la matrice // est liberer faire un close sur la transaction + } else { + // echatellier 20120829 : vidage du cache hibernate + // sinon on fait trop de lecture que la meme transaction + // et le cache hibernate se remplit sans se vider + tx.clearCache(); } } catch (Exception eee) { if (log.isWarnEnabled()) { @@ -579,6 +589,11 @@ // donc mettre la matrice et la connexion dans une map // la matrice dans une weak reference. Des que la matrice // est liberer faire un close sur la transaction + } else { + // echatellier 20120829 : vidage du cache hibernate + // sinon on fait trop de lecture que la meme transaction + // et le cache hibernate se remplit sans se vider + tx.clearCache(); } } catch (TopiaException eee) { if (log.isWarnEnabled()) { Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationExportResultWrapper.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationExportResultWrapper.java 2012-08-27 19:41:06 UTC (rev 3744) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationExportResultWrapper.java 2012-08-30 12:45:25 UTC (rev 3745) @@ -25,6 +25,7 @@ package fr.ifremer.isisfish.simulator; +import static org.nuiton.i18n.I18n._; import java.io.File; import java.util.ArrayList; import java.util.List; @@ -66,9 +67,10 @@ SimulationStorage simulation = context.getSimulationStorage(); SimulationParameter parameters = simulation.getParameter(); File rootDirectory = simulation.getDirectory(); + SimulationControl control = context.getSimulationControl(); // Ici on contantene les 2 listes d'exports - + // first, make export instances based on export // names List<Export> allExports = new ArrayList<Export>(); @@ -95,6 +97,7 @@ // make exports if (!allExports.isEmpty()) { + control.setText(_("isisfish.message.export.export")); File exportDir = SimulationStorage .getResultExportDirectory(rootDirectory); exportDir.mkdirs(); Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2012-08-27 19:41:06 UTC (rev 3744) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2012-08-30 12:45:25 UTC (rev 3745) @@ -48,7 +48,6 @@ import org.nuiton.util.FileUtil; import org.nuiton.util.ObjectUtil; import org.nuiton.util.StringUtil; -import org.nuiton.util.ZipUtil; import fr.ifremer.isisfish.IsisConfig; import fr.ifremer.isisfish.IsisFish; Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SubProcessSimulationLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SubProcessSimulationLauncher.java 2012-08-27 19:41:06 UTC (rev 3744) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SubProcessSimulationLauncher.java 2012-08-30 12:45:25 UTC (rev 3745) @@ -189,7 +189,7 @@ // common args List<String> command = new ArrayList<String>(); command.add(java); - command.add("-Xmx1024M"); + command.add("-Xmx2048M"); // jri args String libraryPath = System.getProperty("java.library.path"); Modified: trunk/src/main/resources/i18n/isis-fish_en_GB.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2012-08-27 19:41:06 UTC (rev 3744) +++ trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2012-08-30 12:45:25 UTC (rev 3745) @@ -544,6 +544,7 @@ isisfish.message.directory.not.exists= isisfish.message.evaluation.finished=evaluation finished isisfish.message.export.done=export done +isisfish.message.export.export=Exporting results isisfish.message.file.already.exists=File %s already exists, do you want overwrite it ? isisfish.message.file.overwrite=File exists, do you want overwrite it ? isisfish.message.import=Import %1$s Modified: trunk/src/main/resources/i18n/isis-fish_fr_FR.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2012-08-27 19:41:06 UTC (rev 3744) +++ trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2012-08-30 12:45:25 UTC (rev 3745) @@ -544,6 +544,7 @@ isisfish.message.directory.not.exists= isisfish.message.evaluation.finished=évaluation terminée isisfish.message.export.done=Export terminé +isisfish.message.export.export=Export des résultats isisfish.message.file.already.exists=Le fichier %s existe, voulez-vous l'écraser ? isisfish.message.file.overwrite=Le fichier existe, voulez-vous l'écraser ? isisfish.message.import=Importer %1$s

1 0