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

r4027 - in trunk: . src/main/java/fr/ifremer/isisfish src/main/java/fr/ifremer/isisfish/datastore src/main/java/fr/ifremer/isisfish/simulator src/main/java/fr/ifremer/isisfish/simulator/launcher src/main/java/fr/ifremer/isisfish/types src/main/java/fr/ifremer/isisfish/ui src/main/java/fr/ifremer/isisfish/ui/simulator src/main/resources/i18n
by bpoussin＠users.forge.codelutin.com June 30, 2014

June 30, 2014

Author: bpoussin Date: 2014-06-30 19:08:42 +0200 (Mon, 30 Jun 2014) New Revision: 4027 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4027 Log: - permit to configure number of step result to save - add memory cache in ResultStorageCSV with configurable size - ResultStorageInMemory is now deprecated - add some information in param tag/value to transfert configuration to server - add some method in TimeStep (add, minus, gap) - add information about ResultStorage used in simulation Modified: trunk/pom.xml trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 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/ResultStorageAbstract.java trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageInMemory.java trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java trunk/src/main/java/fr/ifremer/isisfish/types/TimeStep.java trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/SimulAction.java trunk/src/main/resources/i18n/isis-fish_en_GB.properties trunk/src/main/resources/i18n/isis-fish_fr_FR.properties Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-06-29 18:44:00 UTC (rev 4026) +++ trunk/pom.xml 2014-06-30 17:08:42 UTC (rev 4027) @@ -27,7 +27,7 @@ <dependency> <groupId>org.nuiton</groupId> <artifactId>nuiton-config</artifactId> - <version>3.0-alpha-2</version> + <version>3.0-SNAPSHOT</version> <scope>compile</scope> </dependency> Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-06-29 18:44:00 UTC (rev 4026) +++ trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-06-30 17:08:42 UTC (rev 4027) @@ -54,6 +54,7 @@ import fr.ifremer.isisfish.actions.OtherAction; import fr.ifremer.isisfish.actions.SimulationAction; import fr.ifremer.isisfish.actions.VCSAction; +import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.simulator.SimulationContext; import fr.ifremer.isisfish.simulator.SimulationControl; import fr.ifremer.isisfish.simulator.launcher.InProcessSimulatorLauncher; @@ -63,6 +64,7 @@ import fr.ifremer.isisfish.util.IsisCacheBackend; import fr.ifremer.isisfish.util.IsisCacheBackendOnGuava; import fr.ifremer.isisfish.vcs.VCS; +import org.nuiton.config.OverwriteApplicationConfig; import org.nuiton.math.matrix.DoubleVector; /** @@ -193,10 +195,8 @@ addActionAlias(alias, a.action); } } - } - ////////////////////////////////////////////////// // Methode d'acces aux options ////////////////////////////////////////////////// @@ -831,7 +831,33 @@ saveForUser(); } + /** + * Retourne toutes les configurations specifiques aux simulations. + * Ces configurations sont cotes clients, mais lorsqu'on fait une simulation + * sur un serveur, il faut quelles soient utilisees a la place des valeurs + * du serveur + * + * @return + */ + public Map<String, String> getDefaultSimulationConfig() { + Map<String, String> result = new HashMap<String, String>(); + result.put(Option.SIMULATION_MATRIX_VECTOR_CLASS.key, + getOption(Option.SIMULATION_MATRIX_VECTOR_CLASS.key)); + result.put(Option.SIMULATION_MATRIX_VECTOR_SPARSE_CLASS.key, + getOption(Option.SIMULATION_MATRIX_VECTOR_SPARSE_CLASS.key)); + result.put(Option.SIMULATION_MATRIX_THRESHOLD_USE_SPARSE_CLASS.key, + getOption(Option.SIMULATION_MATRIX_THRESHOLD_USE_SPARSE_CLASS.key)); + result.put(Option.SIMULATION_STORE_RESULT_ON_DISK.key, + getOption(Option.SIMULATION_STORE_RESULT_ON_DISK.key)); + result.put(Option.SIMULATION_STORE_RESULT_CACHE_STEP.key, + getOption(Option.SIMULATION_STORE_RESULT_CACHE_STEP.key)); + + result.put(Option.CACHE_BACKEND_FACTORY_CLASS.key, + getOption(Option.CACHE_BACKEND_FACTORY_CLASS.key)); + + return result; + } /** * @return le dictionnaire des tags par defaut d'une simulation a partir @@ -955,7 +981,8 @@ * @since 4.2.0.2 */ public Class getSimulationMatrixVectorClass() { - Class result = getOptionAsClass(Option.SIMULATION_MATRIX_VECTOR_CLASS.key); + ApplicationConfig config = SimulationContext.get().getConfig(); + Class result = config.getOptionAsClass(Option.SIMULATION_MATRIX_VECTOR_CLASS.key); return result; } @@ -967,7 +994,8 @@ * @since 4.2.0.2 */ public Class getSimulationMatrixVectorSparseClass() { - Class result = getOptionAsClass(Option.SIMULATION_MATRIX_VECTOR_SPARSE_CLASS.key); + ApplicationConfig config = SimulationContext.get().getConfig(); + Class result = config.getOptionAsClass(Option.SIMULATION_MATRIX_VECTOR_SPARSE_CLASS.key); return result; } @@ -978,18 +1006,45 @@ * @since 4.2.0.2 */ public int getSimulationMatrixThresholdUseSparse() { - int result = getOptionAsInt(Option.SIMULATION_MATRIX_THRESHOLD_USE_SPARSE_CLASS.key); + ApplicationConfig config = SimulationContext.get().getConfig(); + int result = config.getOptionAsInt(Option.SIMULATION_MATRIX_THRESHOLD_USE_SPARSE_CLASS.key); return result; } /** + * Indique le nombre de pas qui doivent etre sauve, en partant du dernier pas + * de temps. + * + * @return + * @since 4.2.0.2 + */ + public int getSimulationStoreResultOnDisk() { + ApplicationConfig config = SimulationContext.get().getConfig(); + int result = config.getOptionAsInt(Option.SIMULATION_STORE_RESULT_ON_DISK.key); + return result; + } + + /** + * Indique le nombre de pas qui doivent rester en memoire durant la simulation + * + * @return + * @since 4.2.0.2 + */ + public int getSimulationStoreResultCacheStep() { + ApplicationConfig config = SimulationContext.get().getConfig(); + int result = config.getOptionAsInt(Option.SIMULATION_STORE_RESULT_CACHE_STEP.key); + return result; + } + + /** * Retourne la factory a utilise pour le cache * * @return factory a utilise pour le backend de cache * @since 4.2.1.2 */ public IsisCacheBackend.Factory getCacheBackendFactoryClass() { - IsisCacheBackend.Factory result = getOptionAsObject( + ApplicationConfig config = SimulationContext.get().getConfig(); + IsisCacheBackend.Factory result = config.getOptionAsObject( IsisCacheBackend.Factory.class, Option.CACHE_BACKEND_FACTORY_CLASS.key); return result; } @@ -1030,6 +1085,8 @@ SIMULATION_MATRIX_VECTOR_CLASS("simulation.matrix.vector.class", n("isisfish.config.simulation.matrix.vector.class.description"), DoubleBigVector.class.getName()), SIMULATION_MATRIX_VECTOR_SPARSE_CLASS("simulation.matrix.vector.sparse.class", n("isisfish.config.simulation.matrix.vector.sparse.class.description"), DoubleVector.class.getName()), SIMULATION_MATRIX_THRESHOLD_USE_SPARSE_CLASS("simulation.matrix.threshold.use.sparse.class", n("isisfish.config.simulation.matrix.threshold.use.sparse.class.description"), "1000"), + SIMULATION_STORE_RESULT_ON_DISK("simulation.store.result.ondisk", n("isisfish.config.simulation.store.result.ondisk.description"), "-1"), + SIMULATION_STORE_RESULT_CACHE_STEP("simulation.store.result.cachestep", n("isisfish.config.simulation.store.result.cachestep.description"), "13"), /** 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"), Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java 2014-06-29 18:44:00 UTC (rev 4026) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java 2014-06-30 17:08:42 UTC (rev 4027) @@ -30,7 +30,6 @@ import java.io.IOException; import java.io.RandomAccessFile; import java.util.ArrayList; -import java.util.Collections; import java.util.List; import java.util.Map; import java.util.TreeMap; @@ -50,7 +49,6 @@ import fr.ifremer.isisfish.IsisFishRuntimeException; import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.BitUtil; -import java.util.HashMap; /** * Cette classe permet de conserver des résultats de simulation. Elle permet @@ -73,8 +71,8 @@ protected RandomAccessFile raf; protected long offset; - protected Map<TimeStep, Map<String, ResultMapped>> stepNameResults = - new TreeMap<TimeStep, Map<String, ResultMapped>>(); +// 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>>(); @@ -364,18 +362,18 @@ TimeStep step = r.getStep(); String name = r.getName(); - getResult(step).put(name, r); +// getResult(step).put(name, r); getResult(name).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 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 Map<TimeStep, ResultMapped> getResult(String name) { Map<TimeStep, ResultMapped> result = nameStepResults.get(name); @@ -390,7 +388,7 @@ protected MatrixND readResult(TimeStep step, String name) { MatrixND result = null; - ResultMapped rm = getResult(step).get(name); + ResultMapped rm = getResult(name).get(step); if (rm != null) { result = rm.getMatrix(); } @@ -398,18 +396,18 @@ return result; } - @Override - protected Map<TimeStep, MatrixND> readResult(String name) { - Map<TimeStep, MatrixND> result = Collections.EMPTY_MAP; - Map<TimeStep, ResultMapped> rms = nameStepResults.get(name); - if (rms != null) { - result = new HashMap<TimeStep, MatrixND>(); - for (Map.Entry<TimeStep, ResultMapped> e : rms.entrySet()) { - result.put(e.getKey(), e.getValue().getMatrix()); - } - } - return result; - } +// @Override +// protected Map<TimeStep, MatrixND> readResult(String name) { +// Map<TimeStep, MatrixND> result = Collections.EMPTY_MAP; +// Map<TimeStep, ResultMapped> rms = nameStepResults.get(name); +// if (rms != null) { +// result = new HashMap<TimeStep, MatrixND>(); +// for (Map.Entry<TimeStep, ResultMapped> e : rms.entrySet()) { +// result.put(e.getKey(), e.getValue().getMatrix()); +// } +// } +// return result; +// } @Override protected void writeResult(TimeStep step, String name, MatrixND mat) { Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java 2014-06-29 18:44:00 UTC (rev 4026) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java 2014-06-30 17:08:42 UTC (rev 4027) @@ -42,6 +42,13 @@ public interface ResultStorage extends SimulationResultListener { /** + * Return some information on result storage. Information depend on + * result storage type + * @return + */ + public String getInfo(); + + /** * Permet de savoir si lorsque l'on ajoutera ce resultat, il sera * sauvé ou non. * Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageAbstract.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageAbstract.java 2014-06-29 18:44:00 UTC (rev 4026) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageAbstract.java 2014-06-30 17:08:42 UTC (rev 4027) @@ -28,7 +28,6 @@ import static org.nuiton.i18n.I18n.t; import java.util.ArrayList; -import java.util.Arrays; import java.util.Collection; import java.util.Collections; import java.util.HashSet; @@ -66,6 +65,7 @@ import fr.ifremer.isisfish.simulator.SimulationResultListener; import fr.ifremer.isisfish.types.Month; import fr.ifremer.isisfish.types.TimeStep; +import java.util.LinkedHashMap; import org.nuiton.math.matrix.MatrixFactory; /** @@ -88,6 +88,7 @@ static private Log log = LogFactory.getLog(ResultStorageAbstract.class); protected SimulationStorage simulation = null; + protected EntitySemanticsDecorator decorator; /** result enabled */ transient protected Set<String> enabledResult = null; @@ -96,12 +97,12 @@ * Convertie une entite, month, timestep en string et inversement. * Entity = "TopiaId:Entity.toString" */ - static protected class EntitySemanticsDecorator implements SemanticsDecorator { + static protected class EntitySemanticsDecorator implements SemanticsDecorator<Object, String> { static final private String SEP = ":"; protected TopiaContext tx; /** en cle les representation interne (get) en valeur les valeurs decoree (getKey) */ - protected BidiMap<Object, Object> cache = new DualHashBidiMap<>(); + protected BidiMap<String, Object> cache = new DualHashBidiMap<>(); public EntitySemanticsDecorator() { } @@ -111,39 +112,36 @@ } @Override - public Object decorate(Object internalValue) { + public Object decorate(String internalValue) { Object result = cache.get(internalValue); if (result == null && internalValue != null) { + // on retrouve souvent les memes semantiques dans les matrices + // pour minimiser les chaines en memoire, on prend la representation + // interne avant de l'utiliser comme cle. + internalValue = internalValue.intern(); result = internalValue; - if (internalValue instanceof String) { - // on retrouve souvent les memes semantiques dans les matrices - // pour minimiser les chaines en memoire, on prend la representation - // interne avant de l'utiliser comme cle. - internalValue = ((String)internalValue).intern(); - result = internalValue; - 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 - } + if (StringUtils.startsWith(internalValue, Month.class.getName())) { + String val = StringUtils.substringAfter(internalValue, SEP); + int monthNumber = Integer.parseInt(val); + result = new Month(monthNumber); + } else if (StringUtils.startsWith(internalValue, TimeStep.class.getName())) { + String val = StringUtils.substringAfter(internalValue, SEP); + int stepNumber = Integer.parseInt(val); + result = new TimeStep(stepNumber); + } else if (StringUtils.startsWith(internalValue, "fr.ifremer.isisfish.entities.")) { + if (tx == null) { + result = StringUtils.substringAfter(internalValue, SEP); + } else { + try { + String id = StringUtils.substringBefore(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 } } } @@ -153,8 +151,8 @@ } @Override - public Object undecorate(Object decoratedValue) { - Object result = cache.getKey(decoratedValue); + public String undecorate(Object decoratedValue) { + String result = cache.getKey(decoratedValue); if (result == null && decoratedValue != null) { if (decoratedValue instanceof Month) { result = Month.class.getName() + SEP + ((Month)decoratedValue).getMonthNumber(); @@ -168,7 +166,7 @@ // on retrouve souvent les memes semantiques dans les matrices // pour minimiser les chaines en memoire, on prend la representation // interne avant de l'utiliser comme cle. - cache.put(((String)result).intern(), decoratedValue); + cache.put(result.intern(), decoratedValue); } return result; } @@ -176,20 +174,21 @@ } /** - * Return one result for step and name + * Return one result for step and name. Matrix returned must be undecorated + * (semantics must be string representation of object) * * @param step * @param name * @return */ abstract protected MatrixND readResult(TimeStep step, String name); +// /** +// * Return all available result for name in argument +// * @param name +// * @return +// */ +// abstract protected Map<TimeStep, MatrixND> readResult(String name); /** - * Return all available result for name in argument - * @param name - * @return - */ - abstract protected Map<TimeStep, MatrixND> readResult(String name); - /** * write result * @param step * @param name @@ -217,6 +216,27 @@ return MatrixFactory.getInstance(); } + /** + * 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 ResultStorageAbstract(SimulationStorage simulation) { + this.simulation = simulation; + this.decorator = new EntitySemanticsDecorator(); + } + + /** + * Return some information on result storage. Information depend on + * result storage type + * @return + */ + public String getInfo() { + return getClass().getSimpleName() + " No more information"; + } + protected MatrixND decorate(MatrixND mat, TopiaContext tx) { MatrixND result = null; if (mat != null) { @@ -229,16 +249,39 @@ } /** - * 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 + * Return undecorated version of matrix in argument + * @param mat + * @return new matrix undecorated */ - public ResultStorageAbstract(SimulationStorage simulation) { - this.simulation = simulation; + protected MatrixND undecorate(MatrixND mat) { + MatrixND result = null; + + if (mat != null) { + String name = mat.getName(); + String[] dimNames = mat.getDimensionNames(); + List[] sems = new List[mat.getDimCount()]; + for (int i=0,maxi=sems.length; i<maxi; i++) { + sems[i] = undecorate(mat.getSemantic(i)); + } + result = getMatrixFactory().create(name, sems, dimNames); + result.paste(mat); + } + return result; } + /** + * return new list with undecorate item + * @param l + * @return new list + */ + protected List<String> undecorate(List l) { + ArrayList<String> result = new ArrayList<String>(l.size()); + for (Object o : l) { + result.add(decorator.undecorate(o)); + } + return result; + } + @Override public void delete() { close(); @@ -488,76 +531,68 @@ public MatrixND getMatrix(String name, TopiaContext tx) { log.debug("Get result: " + name); - MatrixND resultMat = null; - Map<TimeStep, MatrixND> results = readResult(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); + // collect de tous les pas de temps possible + 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); - while (step.before(lastStep)) { - step = step.next(); - steps.add(step); - } + } - if (log.isTraceEnabled()) { - log.trace("Steps list : " + steps); + + // collect de toutes les matrices existantes + Map<TimeStep, MatrixND> results = new LinkedHashMap<TimeStep, MatrixND>(); + MatrixND sample = null; + for (TimeStep s : steps) { + MatrixND m = readResult(s, name); + if (m != null) { + results.put(s, m); + sample = m; } + } + // creation des dimensions + String[] dimNames = new String[1 + sample.getDimCount()]; + dimNames[0] = t("isisfish.common.date"); + for (int i = 1; i < dimNames.length; i++) { + dimNames[i] = sample.getDimensionName(i - 1); + } - MatrixND mat = results.values().iterator().next(); + // collect des semantics. +1 pour les dates + List[] sem = new List[1 + sample.getDimCount()]; + sem[0] = steps; - // recuperation des noms des dimensions - String[] dimNames = new String[1 + mat.getDimCount()]; - dimNames[0] = t("isisfish.common.date"); - for (int i = 1; i < dimNames.length; i++) { - dimNames[i] = mat.getDimensionName(i - 1); - } + for (int i = 1; i < sem.length; i++) { + sem[i] = new HashList(); + } - // 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 (MatrixND m : results.values()) { + if (m != null) { + for (int s = 0; s < m.getDimCount(); s++) { + sem[s + 1].addAll(m.getSemantic(s)); + } } + } - for (MatrixND mattmp : results.values()) { - if (log.isTraceEnabled()) { - log.trace("Ajout de la semantics: " - + Arrays.asList(mattmp.getSemantics())); - } + // creation de la matrice resultat + MatrixND resultMat = getMatrixFactory().create(name, sem, dimNames); - 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)); - } + // recuperation du resultat pour chaque date de la simulation, de Date(0) à lastDate + for (Map.Entry<TimeStep, MatrixND> result : results.entrySet()) { + TimeStep d = result.getKey(); + MatrixND m = result.getValue(); - // creation de la matrice resultat - resultMat = getMatrixFactory().create(name, sem, dimNames); - - // recuperation du resultat pour chaque date de la simulation, de Date(0) à lastDate - for (Map.Entry<TimeStep, MatrixND> result : results.entrySet()) { - TimeStep d = result.getKey(); - mat = result.getValue(); - // 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 }, + // 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 = m.iterator(); mi.next();) { + submat.setValue( + ArrayUtil.concat(new Object[] { d }, mi.getSemanticsCoordinates()), mi.getValue()); - } - } } } Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java 2014-06-29 18:44:00 UTC (rev 4026) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java 2014-06-30 17:08:42 UTC (rev 4027) @@ -1,7 +1,9 @@ package fr.ifremer.isisfish.datastore; +import fr.ifremer.isisfish.IsisFish; import fr.ifremer.isisfish.IsisFishRuntimeException; +import fr.ifremer.isisfish.simulator.SimulationContext; import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.SimpleParser; import java.io.BufferedWriter; @@ -18,6 +20,7 @@ import java.util.Arrays; import java.util.Collections; import java.util.HashMap; +import java.util.LinkedHashMap; import java.util.List; import java.util.Map; import java.util.zip.GZIPInputStream; @@ -31,9 +34,14 @@ import org.nuiton.math.matrix.MatrixND; /** - * Ecrit les resultats dans des fichiers au format pseudo csv compresser (gz) - * Seule les valeurs differentes de 0 sont ecrite dans le fichier + * Ecrit les resultats dans des fichiers au format pseudo csv compresse (gz) + * Seules les valeurs differentes de 0 sont ecrites dans le fichier. + * + * Il est possible de modifier via la configuration: + * - le nombre de TimeStep en cache + * - de definir le nombre de TimeStep a conserver sur disque * + * * Format d'une matrice: * <pre> * # commentaire @@ -75,13 +83,47 @@ static final private Charset charset = Charset.forName("UTF-8"); - protected EntitySemanticsDecorator decorator; + /** number of step result to store on disk. 0 for none, negative for all result */ + protected int storeOnDiskStep = -1; + /** number of step in cache */ + protected int cacheStep = 13; // default to 13 months + /** nombre total de resultat */ + protected int numberOfResult = 0; + /** nombre de resultat reellement stocke sur disque */ + protected int numberOfResultOnDisk = 0; + /** le nombre de resultat demande qui n'etait pas dans le pas de temps courant */ + protected int numberOfPastResultAsked = 0; + /** le plus vieux pas de temps demande par rapport au pas de temps courant */ + protected int maxGapWithCurrentStep = 0; + + LinkedHashMap<TimeStep, Map<String, MatrixND>> cache = + new LinkedHashMap<TimeStep, Map<String, MatrixND>>() { + private static final long serialVersionUID = 1L; + @Override + protected boolean removeEldestEntry(Map.Entry eldest) { + return size() > cacheStep; + } + }; + + public ResultStorageCSV(SimulationStorage simulation) { super(simulation); - decorator = new EntitySemanticsDecorator(); + + storeOnDiskStep = IsisFish.config.getSimulationStoreResultOnDisk(); + cacheStep = IsisFish.config.getSimulationStoreResultCacheStep(); } + @Override + public String getInfo() { + return String.format( + "ResultStorageCSV:\n" + + "\t%s results written to disk on a total of %s\n" + + "\t%s results read outside of current step\n" + + "\tthe oldest step was %s step before current step\n", + numberOfResultOnDisk, numberOfResult, numberOfPastResultAsked, maxGapWithCurrentStep); + } + /** * donne le repertoire de stockage des resultats * @return @@ -106,10 +148,6 @@ return file; } - protected MatrixND readMatrix(File file) throws IOException { - return readMatrix(file.getPath()); - } - protected MatrixND readMatrix(String file) throws IOException { MatrixND result = null; LineNumberReader in = null; @@ -195,90 +233,145 @@ @Override protected MatrixND readResult(TimeStep step, String name) { - File file = getMatrixFile(step, name); + // un peu de statistique + TimeStep currentStep = SimulationContext.get().getSimulationControl().getStep(); + if (!step.equals(currentStep)) { + numberOfPastResultAsked++; + maxGapWithCurrentStep = Math.max(maxGapWithCurrentStep, currentStep.gap(step)); + } + MatrixND result = null; - if (file.exists()) { - try { - result = readMatrix(file); - } catch (IOException eee) { - log.error("Can't read result file: " + file, eee); + + // try to get in cache first + if(cache.containsKey(step)) { + result = getCacheForStep(step).get(name); + } + + // if not found looking for result on disk + if (result == null) { + File file = getMatrixFile(step, name); + if (file.exists()) { + try { + result = readMatrix(file.getPath()); + } catch (IOException eee) { + log.error("Can't read result file: " + file, eee); + } } } return result; } - @Override - protected Map<TimeStep, MatrixND> readResult(String name) { - File dir = getMatrixDirectory(name); - String[] files = dir.list(); +// @Override +// protected Map<TimeStep, MatrixND> readResult(String name) { +// File dir = getMatrixDirectory(name); +// String[] files = dir.list(); +// +// Map<TimeStep, MatrixND> result = new HashMap<TimeStep, MatrixND>(); +// for(String file : files) { +// try { +// TimeStep step = getTimeStep(file); +// if (step != null) { +// MatrixND mat = readResult(step, name); +// if (mat != null) { +// result.put(step, mat); +// } +// } +// } catch (Exception eee) { +// log.error("Can't read result file: " + file, eee); +// } +// } +// return result; +// } - Map<TimeStep, MatrixND> result = new HashMap<TimeStep, MatrixND>(); - for(String file : files) { - try { - TimeStep step = getTimeStep(file); - if (step != null) { - MatrixND mat = readMatrix(dir + File.separator + file); - if (mat != null) { - result.put(step, mat); - } - } - } catch (Exception eee) { - log.error("Can't read result file: " + file, eee); - } + /** Le pas de temps a partir duquel il faut sauver les resultats sur disque*/ + protected TimeStep startDiskStep = null; + + /** + * Indique s'il faut sauver sur disque les resultats + * @param step + * @return + */ + protected boolean isDiskResult(TimeStep step) { + if (startDiskStep == null) { + startDiskStep = getLastStep().minus(storeOnDiskStep); } + return storeOnDiskStep < 0 || startDiskStep.before(step); + } + + protected Map<String, MatrixND> getCacheForStep(TimeStep step) { + Map<String, MatrixND> result = cache.get(step); + if (result == null) { + result = new HashMap<String, MatrixND>(); + cache.put(step, result); + } return result; } + @Override protected void writeResult(TimeStep step, String name, MatrixND mat) { - File file = getMatrixFile(step, name); - file.getParentFile().mkdirs(); - PrintWriter out = null; - try { - out = new PrintWriter(new BufferedWriter(new OutputStreamWriter( - new GZIPOutputStream(new FileOutputStream(file)), - charset - ))); + // copy and undecorate matrix + mat = undecorate(mat); + + // add mat in cache + getCacheForStep(step).put(name, mat); - out.print(name); - out.println(); + // for statistics + numberOfResult++; - List[] sems = mat.getSemantics(); - for (int i=0, maxi=sems.length; i<maxi; i++) { - String dimName = mat.getDimensionName(i); - out.print(dimName); + // write mat on disk + if (isDiskResult(step)) { + // for statistics + numberOfResultOnDisk++; + + File file = getMatrixFile(step, name); + file.getParentFile().mkdirs(); + PrintWriter out = null; + try { + out = new PrintWriter(new BufferedWriter(new OutputStreamWriter( + new GZIPOutputStream(new FileOutputStream(file)), + charset + ))); - List l = sems[i]; - char sep = ':'; - for (Object o : l) { - out.print(sep); - out.print(decorator.undecorate(o)); - sep = ';'; - } + out.print(name); out.println(); - } - // blank line to separate header and data - out.println(); + List[] sems = mat.getSemantics(); + for (int i=0, maxi=sems.length; i<maxi; i++) { + String dimName = mat.getDimensionName(i); + out.print(dimName); - for (MatrixIterator i = mat.iteratorNotZero(); i.hasNext();) { - i.next(); - int[] pos = i.getCoordinates(); - double value = i.getValue(); - for (int p : pos) { - out.print(p); - out.print(';'); + List l = sems[i]; + char sep = ':'; + for (Object o : l) { + out.print(sep); + out.print(o); + sep = ';'; + } + out.println(); } - out.print(value); + + // blank line to separate header and data out.println(); + + for (MatrixIterator i = mat.iteratorNotZero(); i.hasNext();) { + i.next(); + int[] pos = i.getCoordinates(); + double value = i.getValue(); + for (int p : pos) { + out.print(p); + out.print(';'); + } + out.print(value); + out.println(); + } + + } catch (Exception eee) { + throw new IsisFishRuntimeException("Can't write result: " + file, eee); + } finally { + IOUtils.closeQuietly(out); } - - } catch (Exception eee) { - throw new IsisFishRuntimeException("Can't write result: " + file, eee); - } finally { - IOUtils.closeQuietly(out); } - } @Override Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageInMemory.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageInMemory.java 2014-06-29 18:44:00 UTC (rev 4026) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageInMemory.java 2014-06-30 17:08:42 UTC (rev 4027) @@ -52,6 +52,8 @@ * * Mise a jour: $Date$ * par : $Author$ + * + * @deprecated ResultStorageCSV now support no storage and in memory usage */ public class ResultStorageInMemory extends ResultStorageAbstract { @@ -103,7 +105,7 @@ @Override protected void writeResult(TimeStep step, String name, MatrixND mat) { - MatrixND newMat = mat.copy(); + MatrixND newMat = undecorate(mat); Map<String, MatrixND> mats = data.get(step); if (mats == null) { mats = new HashMap<String, MatrixND>(); @@ -152,21 +154,21 @@ return result; } - /* (non-Javadoc) - * @see fr.ifremer.isisfish.datastore.ResultStorage#getMatrix(java.lang.String) - */ - @Override - public Map<TimeStep, MatrixND> readResult(String name) { - Map<TimeStep, MatrixND> result = new LinkedHashMap<TimeStep, MatrixND>(); - for (Map.Entry<TimeStep, Map<String, MatrixND>> e : data.entrySet()) { - TimeStep ts = e.getKey(); - MatrixND mat = e.getValue().get(name); - if (mat != null) { - result.put(ts, mat); - } - } +// /* (non-Javadoc) +// * @see fr.ifremer.isisfish.datastore.ResultStorage#getMatrix(java.lang.String) +// */ +// @Override +// public Map<TimeStep, MatrixND> readResult(String name) { +// Map<TimeStep, MatrixND> result = new LinkedHashMap<TimeStep, MatrixND>(); +// for (Map.Entry<TimeStep, Map<String, MatrixND>> e : data.entrySet()) { +// TimeStep ts = e.getKey(); +// MatrixND mat = e.getValue().get(name); +// if (mat != null) { +// result.put(ts, mat); +// } +// } +// +// return result; +// } - return result; - } - } Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-06-29 18:44:00 UTC (rev 4026) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-06-30 17:08:42 UTC (rev 4027) @@ -43,6 +43,8 @@ import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.IsisCache; import fr.ifremer.isisfish.util.Trace; +import org.nuiton.config.ApplicationConfig; +import org.nuiton.config.OverwriteApplicationConfig; import org.nuiton.math.matrix.MatrixFactory; /** @@ -69,6 +71,8 @@ /** to use log facility, just put in your code: log.info(\"...\"); */ private static Log log = LogFactory.getLog(SimulationContext.class); + /** configuration for current simulation (some value of config is overwrited for simulation) */ + protected ApplicationConfig config; protected Map<String, Object> values = new HashMap<String, Object>(); protected SimulationStorage simulation = null; protected SimulationControl simulationControl = null; @@ -103,7 +107,17 @@ }; protected SimulationContext() { - // force matrix backend for this simulation + } + + /** + * init SimulationContext for simulation. + * + */ + public void initForSimulation() { + // must be done after setSimulationStorage because config looking for + // value in simulation parameter via SimulationContext + + // force matrix backend for this simulationcontext MatrixFactory.initMatrixFactoryThreadLocal( IsisFish.config.getSimulationMatrixVectorClass(), IsisFish.config.getSimulationMatrixVectorSparseClass(), @@ -111,6 +125,8 @@ } /** + * Return SimulationContext if not created, create new context without + * initialisation needed for simulation * @return simulation context for the current simulation (current thread) */ public static SimulationContext get() { @@ -132,6 +148,27 @@ } /** + * Get specifique ApplicationConfig for current thread.simulation. + * Needed for simulation some configurations values are overwrited by + * simulation parameter tag/value + * + * @return + */ + public ApplicationConfig getConfig() { + if (config == null) { + if (getSimulationStorage()!= null) { + // in simulation, tag/value must be in config for simulation option + Map<String, String> tv = getSimulationStorage().getParameter().getTagValue(); + config = new OverwriteApplicationConfig(IsisFish.config, tv); + } else { + config = IsisFish.config; + } + } + return config; + } + + + /** * Add simulation listener, if listener is {@link SimulationResultListener}, it's * automatically added as listener on {@link ResultManager} * @param l Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2014-06-29 18:44:00 UTC (rev 4026) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2014-06-30 17:08:42 UTC (rev 4027) @@ -354,6 +354,7 @@ // Creation et initialisation du context de simulation // SimulationContext context = SimulationContext.get(); + context.setSimulationControl(control != null ? control : new SimulationControl(simulation.getName())); @@ -372,7 +373,7 @@ // is simulation context context.setScriptDirectory(rootDirectory); context.setSimulationStorage(simulation); - + // Warning : Rule have to be instanciated after aspect definition classLoader.deploy(RuleAspect.class); @@ -381,6 +382,10 @@ // forceReload, save all modification in parameter and reread it parameters = simulation.getForceReloadParameter(); + // must be done after setSimulationStorage because config looking for + // value in simulation parameter via SimulationContext + context.initForSimulation(); + // // Activation de l'OAP demandée // @@ -425,9 +430,8 @@ String matrixBackend = MatrixFactory.getInstance().getVectorClass().getName(); String matrixSparseBackend = MatrixFactory.getInstance().getSparseVectorClass().getName(); int threshold = MatrixFactory.getInstance().getThresholdSparse(); - simulation.getInformation().addInformation("Matrix backend: " + log.info("Matrix backend: " + matrixBackend + " and " + matrixSparseBackend + " threshold: " + threshold); - log.info("Matrix backend: " + matrixBackend); simulatorObject.simulate(context); // @@ -465,6 +469,7 @@ if (parameters.isSensitivityAnalysisOnlyKeepFirst() && !control.getId().endsWith("_0")) { resultStorage.delete(); } + simulation.getInformation().addInformation(resultStorage.getInfo()); resultStorage.close(); } catch (OutOfMemoryError eee) { Modified: trunk/src/main/java/fr/ifremer/isisfish/types/TimeStep.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/types/TimeStep.java 2014-06-29 18:44:00 UTC (rev 4026) +++ trunk/src/main/java/fr/ifremer/isisfish/types/TimeStep.java 2014-06-30 17:08:42 UTC (rev 4027) @@ -85,6 +85,34 @@ } /** + * Return new TimeStep equals to this.step + number + * @param number number of step to add + * @return new TimeStep + */ + public TimeStep add(int number) { + return new TimeStep(step + number); + } + + /** + * Return new TimeStep equals to this.step - number + * @param number number of step to remove + * @return new TimeStep + */ + public TimeStep minus(int number) { + return new TimeStep(step - number); + } + + /** + * Return number of step between current TimeStep and other TimeStep in argument + * (this - other) + * @param other + * @return + */ + public int gap(TimeStep other) { + return step - other.step; + } + + /** * Method next retourne une nouvelle date qui est la date suivante de la * date courante. la date courante n'est pas modifier. * Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java 2014-06-29 18:44:00 UTC (rev 4026) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java 2014-06-30 17:08:42 UTC (rev 4027) @@ -229,6 +229,8 @@ modelBuilder.addOption(IsisConfig.Option.SIMULATION_MATRIX_VECTOR_SPARSE_CLASS); modelBuilder.addOption(IsisConfig.Option.SIMULATION_MATRIX_THRESHOLD_USE_SPARSE_CLASS); modelBuilder.addOption(IsisConfig.Option.MAPPED_RESULT_MATRIX_VECTOR_CLASS); + modelBuilder.addOption(IsisConfig.Option.SIMULATION_STORE_RESULT_ON_DISK); + modelBuilder.addOption(IsisConfig.Option.SIMULATION_STORE_RESULT_CACHE_STEP); // category database vcs modelBuilder.addCategory(t("isisfish.config.category.officialvcs"), t("isisfish.config.category.officialvcs.description")); Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/SimulAction.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/SimulAction.java 2014-06-29 18:44:00 UTC (rev 4026) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/SimulAction.java 2014-06-30 17:08:42 UTC (rev 4027) @@ -99,6 +99,8 @@ import fr.ifremer.isisfish.ui.sensitivity.wizard.SensitivityWizardHandler; import fr.ifremer.isisfish.ui.util.ErrorHelper; import fr.ifremer.isisfish.ui.widget.editor.ScriptParameterDialog; +import java.util.HashMap; +import java.util.LinkedHashMap; /** * SimulAction. @@ -152,8 +154,12 @@ List<String> resultNames = getResultNames(); // put default value in param param.setSimulatorName(IsisFish.config.getSimulatorClassfile()); - param.setTagValue(IsisFish.config.getDefaultTagValueAsMap()); + Map<String, String> tv = new LinkedHashMap<String, String>(); + tv.putAll(IsisFish.config.getDefaultTagValueAsMap()); + tv.putAll(IsisFish.config.getDefaultSimulationConfig()); + param.setTagValue(tv); + param.setExportNames(IsisFish.config.getDefaultExportNamesAsList()); List<String> defaultResultNames = IsisFish.config .getDefaultResultNamesAsList(); @@ -987,6 +993,26 @@ return SimulationService.getService().getSimulationLaunchers(); } + protected boolean checkAndPrepare(String fullSimulationId) { + boolean result = !("".equals(fullSimulationId) + || SimulationStorage.localyExists(fullSimulationId) + || SimulationService.getService().exists(fullSimulationId)); + + if (result) { + // force all necessary config simulation in tag value + Map<String, String> m = new HashMap<String, String>( + IsisFish.config.getDefaultSimulationConfig()); + Map<String, String> tv = param.getTagValue(); + m.putAll(tv); + param.setTagValue(m); + } else { + ErrorHelper.showErrorDialog(t("isisfish.simulator.simulaction.badid", + fullSimulationId), null); + } + + return result; + } + /** * Launch automatically the simulation, when is possible (no other simulation) * or wait for the last automatically simulation ended. @@ -1008,12 +1034,7 @@ } try { - if ("".equals(fullSimulationId) - || SimulationStorage.localyExists(fullSimulationId) - || SimulationService.getService().exists(fullSimulationId)) { - ErrorHelper.showErrorDialog(t("isisfish.simulator.simulaction.badid", - fullSimulationId), null); - } else { + if (checkAndPrepare(fullSimulationId)) { SimulationService.getService().submit(fullSimulationId, param, launcher, 0); } @@ -1051,12 +1072,7 @@ } try { - if ("".equals(fullSimulationId) - || SimulationStorage.localyExists(fullSimulationId) - || SimulationService.getService().exists(fullSimulationId)) { - ErrorHelper.showErrorDialog(t("isisfish.simulator.simulaction.badid", - fullSimulationId), null); - } else { + if (checkAndPrepare(fullSimulationId)) { DesignPlan designPlan = new DesignPlan(); designPlan.setFactorGroup(factorGroup); SimulationService.getService().submit(fullSimulationId, param, Modified: trunk/src/main/resources/i18n/isis-fish_en_GB.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2014-06-29 18:44:00 UTC (rev 4026) +++ trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2014-06-30 17:08:42 UTC (rev 4027) @@ -229,6 +229,11 @@ isisfish.config.main.userMail.description=User email address isisfish.config.main.userName.description=User name isisfish.config.mapped.result.matrix.vector.class.description= +isisfish.config.simulation.matrix.threshold.use.sparse.class.description= +isisfish.config.simulation.matrix.vector.class.description= +isisfish.config.simulation.matrix.vector.sparse.class.description= +isisfish.config.simulation.store.result.cachestep.description= +isisfish.config.simulation.store.result.ondisk.description= isisfish.config.ssh.key.file=SSH key isisfish.config.ssh.key.file.description=Private SSH key path isisfish.config.title=Preferences Modified: trunk/src/main/resources/i18n/isis-fish_fr_FR.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2014-06-29 18:44:00 UTC (rev 4026) +++ trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2014-06-30 17:08:42 UTC (rev 4027) @@ -229,6 +229,11 @@ isisfish.config.main.userMail.description=le courriel de l'utilisateur isisfish.config.main.userName.description=le nom - prénom de l'utilisateur isisfish.config.mapped.result.matrix.vector.class.description= +isisfish.config.simulation.matrix.threshold.use.sparse.class.description= +isisfish.config.simulation.matrix.vector.class.description= +isisfish.config.simulation.matrix.vector.sparse.class.description= +isisfish.config.simulation.store.result.cachestep.description= +isisfish.config.simulation.store.result.ondisk.description= isisfish.config.ssh.key.file=Clé SSH isisfish.config.ssh.key.file.description=Emplacement de la clé privée SSH isisfish.config.title=Préférences

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r4026 - in trunk/src/main/java/fr/ifremer/isisfish: . aspect datastore simulator simulator/launcher ui util
by bpoussin＠users.forge.codelutin.com June 29, 2014

June 29, 2014

Author: bpoussin Date: 2014-06-29 20:44:00 +0200 (Sun, 29 Jun 2014) New Revision: 4026 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4026 Log: - Add new default ResultStorage (store in pseudo csv compressed file) - old simulation with mapped storage are automaticaly detected - Add configuration for matrix type thresold (dense/sparse: default 1000 value) - guava cache support sparse matrix - factorisation of ResultStorage (ResultMappedStorage, ResultStorageInMemory, ResultStorageCSV) in ResultStorageAbstract - add Trace for equation (but not very useful, because equation name is generated, perhaps need entity to string in name ?) Added: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageAbstract.java trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java trunk/src/main/java/fr/ifremer/isisfish/util/SimpleParser.java Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java trunk/src/main/java/fr/ifremer/isisfish/aspect/TraceAspect.java trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageInMemory.java trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-06-17 16:17:51 UTC (rev 4025) +++ trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-06-29 18:44:00 UTC (rev 4026) @@ -63,6 +63,7 @@ import fr.ifremer.isisfish.util.IsisCacheBackend; import fr.ifremer.isisfish.util.IsisCacheBackendOnGuava; import fr.ifremer.isisfish.vcs.VCS; +import org.nuiton.math.matrix.DoubleVector; /** * Isis fish configuration. @@ -948,10 +949,10 @@ /** * L'implementation de la class gérant les implémentations de vecteur de - * matrice pour les simulations + * matrice pleine pour les simulations * * @return - * @since 4.2.1.1 + * @since 4.2.0.2 */ public Class getSimulationMatrixVectorClass() { Class result = getOptionAsClass(Option.SIMULATION_MATRIX_VECTOR_CLASS.key); @@ -959,6 +960,29 @@ } /** + * L'implementation de la class gérant les implémentations de vecteur de + * matrice creuse pour les simulations + * + * @return + * @since 4.2.0.2 + */ + public Class getSimulationMatrixVectorSparseClass() { + Class result = getOptionAsClass(Option.SIMULATION_MATRIX_VECTOR_SPARSE_CLASS.key); + return result; + } + + /** + * Seuil d'uitilisation des matrices creuse + * + * @return + * @since 4.2.0.2 + */ + public int getSimulationMatrixThresholdUseSparse() { + int result = getOptionAsInt(Option.SIMULATION_MATRIX_THRESHOLD_USE_SPARSE_CLASS.key); + return result; + } + + /** * Retourne la factory a utilise pour le cache * * @return factory a utilise pour le backend de cache @@ -1004,6 +1028,8 @@ // pour les simulations SIMULATION_MATRIX_VECTOR_CLASS("simulation.matrix.vector.class", n("isisfish.config.simulation.matrix.vector.class.description"), DoubleBigVector.class.getName()), + SIMULATION_MATRIX_VECTOR_SPARSE_CLASS("simulation.matrix.vector.sparse.class", n("isisfish.config.simulation.matrix.vector.sparse.class.description"), DoubleVector.class.getName()), + SIMULATION_MATRIX_THRESHOLD_USE_SPARSE_CLASS("simulation.matrix.threshold.use.sparse.class", n("isisfish.config.simulation.matrix.threshold.use.sparse.class.description"), "1000"), /** 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"), Modified: trunk/src/main/java/fr/ifremer/isisfish/aspect/TraceAspect.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/aspect/TraceAspect.java 2014-06-17 16:17:51 UTC (rev 4025) +++ trunk/src/main/java/fr/ifremer/isisfish/aspect/TraceAspect.java 2014-06-29 18:44:00 UTC (rev 4026) @@ -76,6 +76,8 @@ } @Before("execution(* scripts..*(..))" + + " || execution(* fr.ifremer.isisfish.entities..*(..))" + + " || execution(* org.nuiton.math.matrix..*(..))" + " || execution(* simulators..*(..))" + " || execution(* rules..*(..)) " + " || execution(* simulationplans..*(..)) " @@ -86,6 +88,8 @@ @AfterThrowing(throwing = "ex", pointcut = "execution(* scripts..*(..))" + + " || execution(* fr.ifremer.isisfish.entities..*(..))" + + " || execution(* org.nuiton.math.matrix..*(..))" + " || execution(* simulators..*(..))" + " || execution(* rules..*(..)) " + " || execution(* simulationplans..*(..)) " @@ -96,6 +100,8 @@ } @After("execution(* scripts..*(..))" + + " || execution(* fr.ifremer.isisfish.entities..*(..))" + + " || execution(* org.nuiton.math.matrix..*(..))" + " || execution(* simulators..*(..))" + " || execution(* rules..*(..)) " + " || execution(* simulationplans..*(..)) " Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java 2014-06-17 16:17:51 UTC (rev 4025) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java 2014-06-29 18:44:00 UTC (rev 4026) @@ -25,61 +25,32 @@ package fr.ifremer.isisfish.datastore; -import static org.nuiton.i18n.I18n.t; 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.collections4.BidiMap; -import org.apache.commons.collections4.bidimap.DualHashBidiMap; import org.apache.commons.io.IOUtils; -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.DoubleBigVector; 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 fr.ifremer.isisfish.IsisFish; -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; -import fr.ifremer.isisfish.export.Export; -import fr.ifremer.isisfish.export.SensitivityExport; -import fr.ifremer.isisfish.rule.Rule; -import fr.ifremer.isisfish.simulator.Objective; -import fr.ifremer.isisfish.simulator.Optimization; -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 fr.ifremer.isisfish.util.BitUtil; +import java.util.HashMap; /** * Cette classe permet de conserver des résultats de simulation. Elle permet @@ -93,15 +64,13 @@ * Mise a jour: $Date$ * par : $Author$ */ -public class ResultMappedStorage implements SimulationResultListener, - SimulationResultGetter, ResultStorage { // ResultStorage +public class ResultMappedStorage extends ResultStorageAbstract { // ResultStorage /** to use log facility, just put in your code: log.info(\"...\"); */ static private Log log = LogFactory.getLog(ResultMappedStorage.class); - protected MatrixFactory matrixFactory = MatrixFactory.getInstance(DoubleBigVector.class); - - protected SimulationStorage simulation = null; + protected MatrixFactory matrixFactory; + protected RandomAccessFile raf; protected long offset; protected Map<TimeStep, Map<String, ResultMapped>> stepNameResults = @@ -109,91 +78,7 @@ 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; - /** en cle les representation interne (get) en valeur les valeurs decoree (getKey) */ - protected BidiMap<Object, Object> cache = new DualHashBidiMap<>(); - - public EntitySemanticsDecorator() { - } - - public EntitySemanticsDecorator(TopiaContext tx) { - this.tx = tx; - } - - public Object decorate(Object internalValue) { - Object result = cache.get(internalValue); - if (result == null && internalValue != null) { - result = internalValue; - if (internalValue instanceof String) { - // on retrouve souvent les memes semantiques dans les matrices - // pour minimiser les chaines en memoire, on prend la representation - // interne avant de l'utiliser comme cle. - internalValue = ((String)internalValue).intern(); - result = internalValue; - 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) { - 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); - } - // on retrouve souvent les memes semantiques dans les matrices - // pour minimiser les chaines en memoire, on prend la representation - // interne avant de l'utiliser comme cle. - cache.put(((String)result).intern(), 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. @@ -418,13 +303,8 @@ * @param simulation storage to get result */ public ResultMappedStorage(SimulationStorage simulation) throws IOException { - this.simulation = simulation; + super(simulation); - // instanciation de la factory avec l'implementation - // choisie dans la config - Class vectorClass = IsisFish.config.getMappedResultMatrixVectorClass(); - matrixFactory = MatrixFactory.getInstance(vectorClass); - File file = SimulationStorage.getResultFile(simulation.getDirectory()); // il faut toujours ouvrir en 'rw' car sinon les matrices n'arrive pas @@ -434,13 +314,24 @@ // on lit les donnees deja presente offset = 0; while (offset < raf.length()) { - ResultMapped r = new ResultMapped(matrixFactory, raf, offset); + ResultMapped r = new ResultMapped(getMatrixFactory(), raf, offset); storeResult(r); offset += r.size(); } } @Override + protected MatrixFactory getMatrixFactory() { + if (matrixFactory == null) { + // instanciation de la factory avec l'implementation + // choisie dans la config + Class vectorClass = IsisFish.config.getMappedResultMatrixVectorClass(); + matrixFactory = MatrixFactory.getInstance(vectorClass); + } + return matrixFactory; + } + + @Override protected void finalize() throws Throwable { try { raf.close(); @@ -451,7 +342,7 @@ @Override public void delete() { - close(); + super.delete(); File file = SimulationStorage.getResultFile(simulation.getDirectory()); file.delete(); } @@ -474,12 +365,7 @@ 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); + getResult(name).put(step, r); } protected Map<String, ResultMapped> getResult(TimeStep step) { @@ -491,80 +377,42 @@ 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; + result = new TreeMap<TimeStep, ResultMapped>(); + nameStepResults.put(name, result); } return result; } + @Override + protected MatrixND readResult(TimeStep step, String name) { + MatrixND result = null; - 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); + ResultMapped rm = getResult(step).get(name); + if (rm != null) { + result = rm.getMatrix(); } - } - public void addResult(boolean force, TimeStep step, String name, MatrixND mat) throws IsisFishException { - if (force || isEnabled(name)) { - doAddResult(step, name, mat); - } + return result; } - 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)); + @Override + protected Map<TimeStep, MatrixND> readResult(String name) { + Map<TimeStep, MatrixND> result = Collections.EMPTY_MAP; + Map<TimeStep, ResultMapped> rms = nameStepResults.get(name); + if (rms != null) { + result = new HashMap<TimeStep, MatrixND>(); + for (Map.Entry<TimeStep, ResultMapped> e : rms.entrySet()) { + result.put(e.getKey(), e.getValue().getMatrix()); } } + return result; + } + @Override + protected void writeResult(TimeStep step, String name, MatrixND mat) { try { ResultMapped r = new ResultMapped(raf, offset, step, name, mat); storeResult(r); @@ -575,144 +423,15 @@ // temps de simulation, si on ne force pas le sync. // raf.getFD().sync(); } catch (IOException eee) { - log.warn("Can't add result '" + name + "' at step " + step, eee); + throw new IsisFishRuntimeException("Can't write result", 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 && simulation.getSimulationParametersFile().exists()) { - 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.getNewInstance(); - for (String resultName : export.getNecessaryResult()) { - enabledResult.add(resultName); - } - } catch (IsisFishException eee) { - if (log.isWarnEnabled()) { - log.warn(t("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); - } - } - } - - // on objective and optimization - Objective objective = simulation.getParameter().getObjective(); - if (objective != null) { - for (String resultName : objective.getNecessaryResult()) { - enabledResult.add(resultName); - } - } - - Optimization optimization = simulation.getParameter().getOptimization(); - if (optimization != null) { - for (String resultName : optimization.getNecessaryResult()) { - enabledResult.add(resultName); - } - } - - log.info("Enabled result: " + enabledResult); - } - // par defaut on dit qu'on conserve le resultat - boolean result = true; - if (enabledResult != null) { - result = enabledResult.contains(name); - } - return result; + @Override + protected void writeActiveRule(TimeStep step, String name, String params) { + // TODO } - - 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 @@ -722,279 +441,5 @@ 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); - } - - /** - * 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); - } - - /** - * 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) { - tx = getTx(tx); - 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); - } - /* (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. - * - * @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] = t("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 - tx = getTx(tx); - 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; - } - - /** - * 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) - */ - @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; - // } - } Copied: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageAbstract.java (from rev 4023, trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java) =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageAbstract.java (rev 0) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageAbstract.java 2014-06-29 18:44:00 UTC (rev 4026) @@ -0,0 +1,681 @@ +/* + * #%L + * IsisFish + * + * $Id$ + * $HeadURL$ + * %% + * 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 + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ + +package fr.ifremer.isisfish.datastore; + +import static org.nuiton.i18n.I18n.t; + +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 org.apache.commons.collections4.BidiMap; +import org.apache.commons.collections4.bidimap.DualHashBidiMap; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +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 fr.ifremer.isisfish.IsisFishException; +import fr.ifremer.isisfish.IsisFishRuntimeException; +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.Objective; +import fr.ifremer.isisfish.simulator.Optimization; +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 org.nuiton.math.matrix.MatrixFactory; + +/** + * Classe abstraite servant a factoriser tous les traitements commun au differente + * implantation. Lorsqu'on herite de cette classe il reste a definir la lecture + * et l'ecriture reel des resultats (en memoire, en base, binary file, ...) + * + * Created: 24 juin 2014 + * + * @author Benjamin Poussin : poussin(a)codelutin.com + * @version $Revision$ + * + * Mise a jour: $Date$ + * par : $Author$ + */ +public abstract class ResultStorageAbstract implements SimulationResultListener, + SimulationResultGetter, ResultStorage { // ResultStorage + + /** to use log facility, just put in your code: log.info(\"...\"); */ + static private Log log = LogFactory.getLog(ResultStorageAbstract.class); + + protected SimulationStorage simulation = null; + + /** 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; + /** en cle les representation interne (get) en valeur les valeurs decoree (getKey) */ + protected BidiMap<Object, Object> cache = new DualHashBidiMap<>(); + + public EntitySemanticsDecorator() { + } + + public EntitySemanticsDecorator(TopiaContext tx) { + this.tx = tx; + } + + @Override + public Object decorate(Object internalValue) { + Object result = cache.get(internalValue); + if (result == null && internalValue != null) { + result = internalValue; + if (internalValue instanceof String) { + // on retrouve souvent les memes semantiques dans les matrices + // pour minimiser les chaines en memoire, on prend la representation + // interne avant de l'utiliser comme cle. + internalValue = ((String)internalValue).intern(); + result = internalValue; + 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; + } + + @Override + public Object undecorate(Object 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); + } + // on retrouve souvent les memes semantiques dans les matrices + // pour minimiser les chaines en memoire, on prend la representation + // interne avant de l'utiliser comme cle. + cache.put(((String)result).intern(), decoratedValue); + } + return result; + } + + } + + /** + * Return one result for step and name + * + * @param step + * @param name + * @return + */ + abstract protected MatrixND readResult(TimeStep step, String name); + /** + * Return all available result for name in argument + * @param name + * @return + */ + abstract protected Map<TimeStep, MatrixND> readResult(String name); + /** + * write result + * @param step + * @param name + * @param mat + */ + abstract protected void writeResult(TimeStep step, String name, MatrixND mat); + /** + * Write active rule + * @param step + * @param name + * @param params + */ + abstract protected void writeActiveRule(TimeStep step, String name, String params); + /** + * return list of all result name available + * @return + */ + abstract public List<String> getResultName(); + + /** + * sub class can overwrite this method to return specifique factory + * @return + */ + protected MatrixFactory getMatrixFactory() { + return MatrixFactory.getInstance(); + } + + protected MatrixND decorate(MatrixND mat, TopiaContext tx) { + MatrixND result = null; + if (mat != null) { + // on decore la matrice resultat au dernier moment, tous les calcules + // ce font avec les strings + tx = getTx(tx); + result = new MatrixSemanticsDecorator(mat, 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 ResultStorageAbstract(SimulationStorage simulation) { + this.simulation = simulation; + } + + @Override + public void delete() { + close(); + } + + @Override + public void close() { + } + + @Override + public void addResult(TimeStep step, MatrixND mat) throws IsisFishException { + addResult(false, step, mat.getName(), mat); + } + + @Override + public void addResult(TimeStep step, Population pop, MatrixND mat) throws IsisFishException { + addResult(false, step, mat.getName(), pop, mat); + } + + @Override + public void addResult(boolean force, TimeStep step, MatrixND mat) throws IsisFishException { + addResult(force, step, mat.getName(), mat); + } + + @Override + public void addResult(boolean force, TimeStep step, Population pop, MatrixND mat) throws IsisFishException { + addResult(force, step, mat.getName(), pop, mat); + } + + @Override + public void addResult(TimeStep step, String name, Population pop, MatrixND mat) throws IsisFishException { + addResult(false, step, name, pop, mat); + } + + @Override + public void addResult(TimeStep step, String name, MatrixND mat) throws IsisFishException { + addResult(false, step, name, mat); + } + + @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); + } + } + + @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 { + // 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 { + writeResult(step, name, mat); + } catch (Exception 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 + */ + @Override + public boolean isEnabled(String name) { + name = name.trim(); + if (enabledResult == null && simulation.getSimulationParametersFile().exists()) { + 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.getNewInstance(); + Collections.addAll(enabledResult, export.getNecessaryResult()); + } catch (IsisFishException eee) { + if (log.isWarnEnabled()) { + log.warn(t("isisfish.error.instanciate.export", + exportName), eee); + } + } + } + } + + // test on sensitivity export + List<SensitivityExport> sensitivityExports = simulation + .getParameter().getSensitivityExport(); + if (sensitivityExports != null) { + for (SensitivityExport sensitivityExport : sensitivityExports) { + Collections.addAll(enabledResult, sensitivityExport.getNecessaryResult()); + } + } + + // test on rules + List<Rule> rules = simulation.getParameter().getRules(); + if (rules != null) { + for (Rule rule : rules) { + Collections.addAll(enabledResult, rule.getNecessaryResult()); + } + } + + // test on plans + List<SimulationPlan> plans = simulation.getParameter().getSimulationPlans(); + if (plans != null) { + for (SimulationPlan plan : plans) { + Collections.addAll(enabledResult, plan.getNecessaryResult()); + } + } + + // on objective and optimization + Objective objective = simulation.getParameter().getObjective(); + if (objective != null) { + Collections.addAll(enabledResult, objective.getNecessaryResult()); + } + + Optimization optimization = simulation.getParameter().getOptimization(); + if (optimization != null) { + Collections.addAll(enabledResult, optimization.getNecessaryResult()); + } + + log.info("Enabled result: " + enabledResult); + } + // par defaut on dit qu'on conserve le resultat + boolean result = true; + if (enabledResult != null) { + result = enabledResult.contains(name); + } + return result; + } + + + @Override + public void addActiveRule(TimeStep step, Rule rule) throws IsisFishException { + String name = RuleStorage.getName(rule); + String params = RuleStorage.getParamAsString(rule); + writeActiveRule(step, name, params); + } + + /** + * 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. + */ + @Override + public MatrixND getMatrix(TimeStep step, Population pop, String name) { + String newName = name + " " + pop; + 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); + } + + @Override + 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. + */ + @Override + public MatrixND getMatrix(TimeStep step, String name, TopiaContext tx) { + MatrixND mat = readResult(step, name); + mat = decorate(mat, 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. + */ + @Override + public MatrixND getMatrix(Population pop, String name) { + 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. + * + * @param name le nom des resultats dont on veut une matrice globale. + */ + @Override + 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. + */ + @Override + public MatrixND getMatrix(String name, TopiaContext tx) { + log.debug("Get result: " + name); + + MatrixND resultMat = null; + Map<TimeStep, MatrixND> results = readResult(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(); + + // recuperation des noms des dimensions + String[] dimNames = new String[1 + mat.getDimCount()]; + dimNames[0] = t("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 (MatrixND mattmp : results.values()) { + 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 = getMatrixFactory().create(name, sem, dimNames); + + // recuperation du resultat pour chaque date de la simulation, de Date(0) à lastDate + for (Map.Entry<TimeStep, MatrixND> result : results.entrySet()) { + TimeStep d = result.getKey(); + mat = result.getValue(); + // 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()); + } + } + } + } + + resultMat = decorate(resultMat, tx); + return resultMat; + } + + /** + * Get last simulation date. + * + * @return last simulation date + */ + @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 { + 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; + } + + /** + * 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) + */ + @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; + // } + +} Added: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java (rev 0) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java 2014-06-29 18:44:00 UTC (rev 4026) @@ -0,0 +1,303 @@ +package fr.ifremer.isisfish.datastore; + + +import fr.ifremer.isisfish.IsisFishRuntimeException; +import fr.ifremer.isisfish.types.TimeStep; +import fr.ifremer.isisfish.util.SimpleParser; +import java.io.BufferedWriter; +import java.io.File; +import java.io.FileInputStream; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.InputStreamReader; +import java.io.LineNumberReader; +import java.io.OutputStreamWriter; +import java.io.PrintWriter; +import java.nio.charset.Charset; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.zip.GZIPInputStream; +import java.util.zip.GZIPOutputStream; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.nuiton.math.matrix.MatrixIterator; +import org.nuiton.math.matrix.MatrixND; + +/** + * Ecrit les resultats dans des fichiers au format pseudo csv compresser (gz) + * Seule les valeurs differentes de 0 sont ecrite dans le fichier + * + * Format d'une matrice: + * <pre> + * # commentaire + * [nom] + * [nom dimension1]:[semantique1];[semantique2];... + * [nom dimension2]:[semantique1];[semantique2];... + * ... + * [ligne blanche] + * [coordonnee1];[coordonnee2];...;[valeur] + * [coordonnee1];[coordonnee2];...;[valeur] + * [coordonnee1];[coordonnee2];...;[valeur] + * ... + * </pre> + * + * Exemple + * <pre> + * MaMatrice + * Mois:Janvier;Fevrier;Mars + * Ville:Nantes;Paris;Nice + * + * 1;1;2;13.5 + * 0;2;1;4.2 + * </pre> + * + * TODO: + * stat du nombre de demande de resultat or pas de temps courant + * stat sur max ecart entre pas de temps courant et pas de temps demande + * + * @author poussin + * @version $Revision$ + * + * Last update: $Date$ + * by : $Author$ + */ +public class ResultStorageCSV extends ResultStorageAbstract { + + /** to use log facility, just put in your code: log.info(\"...\"); */ + static private Log log = LogFactory.getLog(ResultStorageCSV.class); + + static final private Charset charset = Charset.forName("UTF-8"); + + protected EntitySemanticsDecorator decorator; + + public ResultStorageCSV(SimulationStorage simulation) { + super(simulation); + decorator = new EntitySemanticsDecorator(); + } + + /** + * donne le repertoire de stockage des resultats + * @return + */ + protected File getDirectory() { + File file = SimulationStorage.getResultDirectory(simulation.getDirectory()); + return file; + } + + /** + * Donne le repertoire de stockage pour un certain type de resultat matriciel + * @param name + * @return + */ + protected File getMatrixDirectory(String name) { + File file = new File(getDirectory(), "matrix" + File.separator + name); + return file; + } + + protected File getMatrixFile(TimeStep step, String name) { + File file = new File(getMatrixDirectory(name), step.getStep() + "-" + name + ".csv.gz"); + return file; + } + + protected MatrixND readMatrix(File file) throws IOException { + return readMatrix(file.getPath()); + } + + protected MatrixND readMatrix(String file) throws IOException { + MatrixND result = null; + LineNumberReader in = null; + try { + in = new LineNumberReader(new InputStreamReader( + new GZIPInputStream(new FileInputStream(file)), charset)); + + SimpleParser sp = new SimpleParser(in, true); + + // lecture du nom de la matrice + String name = sp.readString('\n'); + + + // lecture du nom des dimensions et des semantics + List<String> dimNames = new ArrayList<String>(); + List<List<String>> semantics = new ArrayList<List<String>>(); + + String dimName = sp.readString(':'); + while (!sp.isEOL() || StringUtils.isNotBlank(dimName)) { + dimNames.add(dimName); + List<String> sems = new ArrayList<String>(); + semantics.add(sems); + while (!sp.isEOL()) { + String sem = sp.readString(';'); + sems.add(sem); + } + dimName = sp.readString(':'); + } + + // creation de la matrice resultat avec les infos collectes + result = getMatrixFactory().create(name, + semantics.toArray(new List[semantics.size()]), + dimNames.toArray(new String[dimNames.size()])); + + + // lecture des data + int nbDim = dimNames.size(); + int[] coord = new int[nbDim]; + + while (!sp.isEOF()) { + for (int i=0; i<nbDim; i++) { + coord[i] = sp.readInt(';'); + } + double v = sp.readDouble(';'); + result.setValue(coord, v); + } + + } finally { + IOUtils.closeQuietly(in); + } + + return result; + } + + /** + * Extract and create TimeStep from file name. If file name doesn't contains + * TimeStep null is returned + * @param file + * @return + */ + protected TimeStep getTimeStep(String file) { + TimeStep result = null; + try { + String num = StringUtils.substringBefore(file, "-"); + int step = Integer.parseInt(num); + result = new TimeStep(step); + } catch(NumberFormatException eee) { + log.error("File doesn't contains step information: " + file, eee); + } + return result; + } + + @Override + public void delete() { + super.delete(); + try { + File file = getDirectory(); + FileUtils.deleteDirectory(file); + } catch (IOException eee) { + throw new IsisFishRuntimeException("Can't delete results", eee); + } + } + + @Override + protected MatrixND readResult(TimeStep step, String name) { + File file = getMatrixFile(step, name); + MatrixND result = null; + if (file.exists()) { + try { + result = readMatrix(file); + } catch (IOException eee) { + log.error("Can't read result file: " + file, eee); + } + } + return result; + } + + @Override + protected Map<TimeStep, MatrixND> readResult(String name) { + File dir = getMatrixDirectory(name); + String[] files = dir.list(); + + Map<TimeStep, MatrixND> result = new HashMap<TimeStep, MatrixND>(); + for(String file : files) { + try { + TimeStep step = getTimeStep(file); + if (step != null) { + MatrixND mat = readMatrix(dir + File.separator + file); + if (mat != null) { + result.put(step, mat); + } + } + } catch (Exception eee) { + log.error("Can't read result file: " + file, eee); + } + } + return result; + } + + @Override + protected void writeResult(TimeStep step, String name, MatrixND mat) { + File file = getMatrixFile(step, name); + file.getParentFile().mkdirs(); + PrintWriter out = null; + try { + out = new PrintWriter(new BufferedWriter(new OutputStreamWriter( + new GZIPOutputStream(new FileOutputStream(file)), + charset + ))); + + out.print(name); + out.println(); + + List[] sems = mat.getSemantics(); + for (int i=0, maxi=sems.length; i<maxi; i++) { + String dimName = mat.getDimensionName(i); + out.print(dimName); + + List l = sems[i]; + char sep = ':'; + for (Object o : l) { + out.print(sep); + out.print(decorator.undecorate(o)); + sep = ';'; + } + out.println(); + } + + // blank line to separate header and data + out.println(); + + for (MatrixIterator i = mat.iteratorNotZero(); i.hasNext();) { + i.next(); + int[] pos = i.getCoordinates(); + double value = i.getValue(); + for (int p : pos) { + out.print(p); + out.print(';'); + } + out.print(value); + out.println(); + } + + } catch (Exception eee) { + throw new IsisFishRuntimeException("Can't write result: " + file, eee); + } finally { + IOUtils.closeQuietly(out); + } + + } + + @Override + protected void writeActiveRule(TimeStep step, String name, String params) { + // TODO + } + + @Override + public List<String> getResultName() { + File dir = getMatrixDirectory(""); + String[] files = dir.list(); + List<String> result; + if (files != null) { + Arrays.sort(files); + result = Arrays.asList(files); + } else { + result = Collections.EMPTY_LIST; + } + return result; + } + +} Property changes on: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageInMemory.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageInMemory.java 2014-06-17 16:17:51 UTC (rev 4025) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageInMemory.java 2014-06-29 18:44:00 UTC (rev 4026) @@ -25,37 +25,17 @@ package fr.ifremer.isisfish.datastore; -import static org.nuiton.i18n.I18n.t; 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.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.util.ArrayUtil; -import org.nuiton.util.HashList; - -import fr.ifremer.isisfish.IsisFishException; -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.Objective; -import fr.ifremer.isisfish.simulator.Optimization; -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; import java.util.HashMap; import java.util.LinkedHashMap; import java.util.LinkedList; @@ -73,14 +53,13 @@ * Mise a jour: $Date$ * par : $Author$ */ -public class ResultStorageInMemory implements SimulationResultGetter, ResultStorage { +public class ResultStorageInMemory extends ResultStorageAbstract { /** to use log facility, just put in your code: log.info(\"...\"); */ static private Log log = LogFactory.getLog(ResultStorageInMemory.class); final static public String MAX_TIME_STEP = "ResultStorageInMemory.maxTimeStep"; protected int maxTimeStep = 12; // default to 1 year - protected SimulationStorage simulation = null; LinkedHashMap<TimeStep, Map<String, MatrixND>> data = new LinkedHashMap<TimeStep, Map<String, MatrixND>>() { private static final long serialVersionUID = 1L; @@ -90,7 +69,7 @@ } }; - LinkedHashMap<TimeStep, List<Rule>> rules = new LinkedHashMap<TimeStep, List<Rule>>() { + LinkedHashMap<TimeStep, List<String>> rules = new LinkedHashMap<TimeStep, List<String>>() { private static final long serialVersionUID = 1L; @Override protected boolean removeEldestEntry(Map.Entry eldest) { @@ -98,10 +77,6 @@ } }; - - /** result enabled */ - transient protected Set<String> enabledResult = null; - /** * Les ResultStorage ne doivent pas etre instancier directement, mais * recuperer a partir d'un @@ -110,187 +85,24 @@ * @param simulation storage to get result */ public ResultStorageInMemory(SimulationStorage simulation) { - this.simulation = simulation; + super(simulation); maxTimeStep = Integer.parseInt(simulation.getParameter().getTagValue().get(MAX_TIME_STEP)); } @Override public void delete() { + super.delete(); data.clear(); } @Override - public void close() { - // do nothing, closed by simulation storage closing + protected MatrixND decorate(MatrixND mat, TopiaContext tx) { + // for in memory do nothing, matrice has already semantics (not string) + return mat; } - /* (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.getNewInstance(); - for (String resultName : export.getNecessaryResult()) { - enabledResult.add(resultName); - } - } catch (IsisFishException eee) { - if (log.isWarnEnabled()) { - log.warn(t("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); - } - } - } - - // on objective and optimization - Objective objective = simulation.getParameter().getObjective(); - if (objective != null) { - for (String resultName : objective.getNecessaryResult()) { - enabledResult.add(resultName); - } - } - - Optimization optimization = simulation.getParameter().getOptimization(); - if (optimization != null) { - for (String resultName : optimization.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 { - // 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) + protected void writeResult(TimeStep step, String name, MatrixND mat) { MatrixND newMat = mat.copy(); Map<String, MatrixND> mats = data.get(step); if (mats == null) { @@ -299,24 +111,17 @@ } mats.put(name, newMat); - } + } - /* (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 { - List<Rule> list = rules.get(step); + protected void writeActiveRule(TimeStep step, String name, String params) { + List<String> list = rules.get(step); if (list == null) { - list = new LinkedList<Rule>(); + list = new LinkedList<String>(); rules.put(step, list); } - list.add(rule); - -// result.setActiveRuleStep(step); -// result.setName(RuleStorage.getName(rule)); -// result.setParam(RuleStorage.getParamAsString(rule)); + list.add(name); } /* (non-Javadoc) @@ -335,19 +140,10 @@ } /* (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) { + public MatrixND readResult(TimeStep step, String name) { MatrixND result = null; Map<String, MatrixND> mats = data.get(step); if (mats != null) { @@ -356,160 +152,21 @@ return result; } - @Override - public MatrixND getMatrix(TimeStep step, String name, TopiaContext tx) { - return getMatrix(step, name); - } - /* (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 result = null; - - List<TimeStep> steps = new ArrayList<TimeStep>(); - Map<TimeStep, MatrixND> mats = new LinkedHashMap<TimeStep, MatrixND>(); - MatrixND matExample = null; + public Map<TimeStep, MatrixND> readResult(String name) { + Map<TimeStep, MatrixND> result = new LinkedHashMap<TimeStep, MatrixND>(); for (Map.Entry<TimeStep, Map<String, MatrixND>> e : data.entrySet()) { TimeStep ts = e.getKey(); MatrixND mat = e.getValue().get(name); if (mat != null) { - steps.add(ts); - mats.put(ts, mat); - matExample = mat; + result.put(ts, mat); } } - if (mats.size() > 0) { - // recuperation des noms des dimensions - String[] dimNames = new String[1 + matExample.getDimCount()]; - dimNames[0] = t("isisfish.common.date"); - for (int i = 1; i < dimNames.length; i++) { - dimNames[i] = matExample.getDimensionName(i - 1); - } - - // creation de la semantique pour la matrice resultat. +1 pour les dates - List[] sem = new List[1 + matExample.getDimCount()]; - sem[0] = steps; - - for (int i = 1; i < sem.length; i++) { - sem[i] = new HashList(); - } - - for (MatrixND mattmp : mats.values()) { - 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 - result = MatrixFactory.getInstance().create(name, sem, dimNames); - - // recuperation du resultat pour chaque date de la simulation, de Date(0) à lastDate - for (Map.Entry<TimeStep, MatrixND> e : mats.entrySet()) { - TimeStep d = e.getKey(); - MatrixND mat = e.getValue(); - // on recupere dans la matrice resultat l'endroit on il faut - // mettre la matrice - MatrixND submat = result.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()); - } - } - } - return result; } - /* (non-Javadoc) - * @see fr.ifremer.isisfish.datastore.ResultStorage#getMatrix(java.lang.String, org.nuiton.topia.TopiaContext) - */ - @Override - public MatrixND getMatrix(String name, TopiaContext tx) { - return getMatrix(name); - } - - /* (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 { - 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 = getMatrix(step, name); - 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 = getMatrix(name); - 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) { - } - } Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java 2014-06-17 16:17:51 UTC (rev 4025) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java 2014-06-29 18:44:00 UTC (rev 4026) @@ -78,6 +78,7 @@ 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_DIRECTORY = "results"; 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"; @@ -260,6 +261,21 @@ } /** + * Retourne le fichier de stockage des resultats + * de la simulation. + * + * @param root le repertoire de stockage de la simulation + * @return + */ + public static File getResultDirectory(File root) { + File result = new File(root, RESULT_DIRECTORY); + if (!result.exists()) { + result.mkdirs(); + } + return result; + } + + /** * Retourne le fichier de stockage des parametres de la simulation courante. * * @return parameter file @@ -523,7 +539,14 @@ resultStorage = new ResultStorageInMemory(this); } else { try { - resultStorage = new ResultMappedStorage(this); + if (getResultFile(getDirectory()).exists()) { + // if result.mapped exist, use ResultMappedStorage + // need to read old simulation + resultStorage = new ResultMappedStorage(this); + } else { + // else use ResultStorageCSV, the new default result storage + resultStorage = new ResultStorageCSV(this); + } } catch (IOException ex) { throw new StorageException("Can't get storage", ex); } Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-06-17 16:17:51 UTC (rev 4025) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-06-29 18:44:00 UTC (rev 4026) @@ -25,7 +25,6 @@ package fr.ifremer.isisfish.simulator; -import fr.ifremer.isisfish.IsisConfig; import fr.ifremer.isisfish.IsisFish; import java.io.File; import java.util.HashMap; @@ -105,7 +104,10 @@ protected SimulationContext() { // force matrix backend for this simulation - MatrixFactory.initMatrixFactoryThreadLocal(IsisFish.config.getSimulationMatrixVectorClass()); + MatrixFactory.initMatrixFactoryThreadLocal( + IsisFish.config.getSimulationMatrixVectorClass(), + IsisFish.config.getSimulationMatrixVectorSparseClass(), + IsisFish.config.getSimulationMatrixThresholdUseSparse()); } /** Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2014-06-17 16:17:51 UTC (rev 4025) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2014-06-29 18:44:00 UTC (rev 4026) @@ -423,8 +423,10 @@ // context.fireBeforeSimulation(); String matrixBackend = MatrixFactory.getInstance().getVectorClass().getName(); + String matrixSparseBackend = MatrixFactory.getInstance().getSparseVectorClass().getName(); + int threshold = MatrixFactory.getInstance().getThresholdSparse(); simulation.getInformation().addInformation("Matrix backend: " - + matrixBackend); + + matrixBackend + " and " + matrixSparseBackend + " threshold: " + threshold); log.info("Matrix backend: " + matrixBackend); simulatorObject.simulate(context); Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java 2014-06-17 16:17:51 UTC (rev 4025) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java 2014-06-29 18:44:00 UTC (rev 4026) @@ -226,6 +226,8 @@ modelBuilder.addOption(IsisConfig.Option.SIMULATOR_SUB_MAXPROCESS); modelBuilder.addOption(IsisConfig.Option.SIMULATOR_SUB_MAXMEMORY); modelBuilder.addOption(IsisConfig.Option.SIMULATION_MATRIX_VECTOR_CLASS); + modelBuilder.addOption(IsisConfig.Option.SIMULATION_MATRIX_VECTOR_SPARSE_CLASS); + modelBuilder.addOption(IsisConfig.Option.SIMULATION_MATRIX_THRESHOLD_USE_SPARSE_CLASS); modelBuilder.addOption(IsisConfig.Option.MAPPED_RESULT_MATRIX_VECTOR_CLASS); // category database vcs Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java 2014-06-17 16:17:51 UTC (rev 4025) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java 2014-06-29 18:44:00 UTC (rev 4026) @@ -85,12 +85,9 @@ // on prend le nombre de case de la matrice pour sa taille // on ne tient pas compte des dimensions qui sont des objets // utilises ailleurs - int[] dim = ((MatrixND)value).getDim(); - int size = 1; - for (int i=0; i<dim.length; i++) { - size *= dim[i]; - } - result += size * DOUBLE_SIZE; // size is wrong, because depend on matrix type (float or double) + int size = ((MatrixND)value).getNumberOfAssignedValue(); + // size is wrong, because depend on matrix type (float or double), but approximation is acceptable + result += size * DOUBLE_SIZE; } else if (value instanceof Collection) { // List<Zone|Pop|Str|Metier|Cell> // on prend la taille de la collection, car la donnees Added: trunk/src/main/java/fr/ifremer/isisfish/util/SimpleParser.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/SimpleParser.java (rev 0) +++ trunk/src/main/java/fr/ifremer/isisfish/util/SimpleParser.java 2014-06-29 18:44:00 UTC (rev 4026) @@ -0,0 +1,131 @@ +package fr.ifremer.isisfish.util; + + +import java.io.BufferedReader; +import java.io.IOException; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +/** + * Very simple parse write for efficiency. Input stream must be correct no check + * is done on data. + * + * @author poussin + * @version $Revision$ + * + * Last update: $Date$ + * by : $Author$ + */ +public class SimpleParser { + + /** to use log facility, just put in your code: log.info(\"...\"); */ + static private Log log = LogFactory.getLog(SimpleParser.class); + + protected boolean intern; + protected BufferedReader in; + protected StringBuilder sb = new StringBuilder(); + + protected boolean eof = false; + protected boolean eol = false; + /** + * + * @param in BufferedReader because Reader must support mark and reset + */ + public SimpleParser(BufferedReader in, boolean intern) { + this.in = in; + this.intern = intern; + } + + /** + * + * @return true if end of file + */ + public boolean isEOF() { + return eof; + } + + /** + * + * @return true if end of line + */ + public boolean isEOL() { + return eol; + } + + protected void read(char sep) throws IOException { + eol = false; + sb.setLength(0); + + int i; + while ((i = in.read()) != -1) { + char c = (char)i; + if (c == '\r') { + // try to eat \n after \r + in.mark(1); + c = (char)in.read(); + if (c != '\n') { + in.reset(); + } + eol = true; + break; + } else if (c == '\n') { + eol = true; + break; + } else if (c == sep) { + break; + } else { + sb.append(c); + } + } + + if (i != -1) { + // test if not eof + in.mark(1); + i = in.read(); + in.reset(); + } + eof = i == -1; + } + + public String readString(char sep) throws IOException { + read(sep); + String result = sb.toString(); + if (intern) { + result = result.intern(); + } + return result; + } + + public int readInt(char sep) throws IOException { + read(sep); + int result = parseInt(sb); + return result; + } + + public double readDouble(char sep) throws IOException { + read(sep); + double result = parseDouble(sb); + return result; + } + + protected double parseDouble(StringBuilder s) throws IOException { + return Double.parseDouble(s.toString()); + } + + /** + * custom parseInt: 4 fois plus performant que Integer.parseInt + * ne supporte que les chiffres positif, et la chaine doit forcement etre un nombre valide + * @param sb la chaine representant l'entier + * @return + */ + protected int parseInt(StringBuilder sb) { + int result = 0; + for (int i=0, maxi=sb.length(); i<maxi; i++) { + char c = sb.charAt(i); + result = result * 10 + c - '0'; + } + return result; + } + + +} Property changes on: trunk/src/main/java/fr/ifremer/isisfish/util/SimpleParser.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL

1 0

r4025 - trunk
by echatellier＠users.forge.codelutin.com June 17, 2014

June 17, 2014

Author: echatellier Date: 2014-06-17 18:17:51 +0200 (Tue, 17 Jun 2014) New Revision: 4025 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4025 Log: Fix nuiton-matrix version Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-06-17 15:50:26 UTC (rev 4024) +++ trunk/pom.xml 2014-06-17 16:17:51 UTC (rev 4025) @@ -88,7 +88,7 @@ <dependency> <groupId>org.nuiton.matrix</groupId> <artifactId>nuiton-matrix-gui</artifactId> - <version>2.4.1</version> + <version>2.4.2-SNAPSHOT</version> <scope>compile</scope> </dependency>

1 0

r4024 - in trunk: . src/main/java/fr/ifremer/isisfish src/main/java/fr/ifremer/isisfish/simulator src/main/java/fr/ifremer/isisfish/simulator/launcher src/main/java/fr/ifremer/isisfish/ui
by bpoussin＠users.forge.codelutin.com June 17, 2014

June 17, 2014

Author: bpoussin Date: 2014-06-17 17:50:26 +0200 (Tue, 17 Jun 2014) New Revision: 4024 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4024 Log: add possibility to change matrix backend for simulation in configuration Modified: trunk/pom.xml trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-06-17 15:29:15 UTC (rev 4023) +++ trunk/pom.xml 2014-06-17 15:50:26 UTC (rev 4024) @@ -81,7 +81,7 @@ <dependency> <groupId>org.nuiton.matrix</groupId> <artifactId>nuiton-matrix</artifactId> - <version>2.4.1</version> + <version>2.4.2-SNAPSHOT</version> <scope>compile</scope> </dependency> Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-06-17 15:29:15 UTC (rev 4023) +++ trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-06-17 15:50:26 UTC (rev 4024) @@ -936,7 +936,7 @@ /** * L'implementation de la class gérant les implémentations de vecteur de - * matrice pour les fichiers mappés. + * matrice pour les fichiers mappés pour le rendu des resultats * * @return * @since 4.2.1.1 @@ -947,6 +947,18 @@ } /** + * L'implementation de la class gérant les implémentations de vecteur de + * matrice pour les simulations + * + * @return + * @since 4.2.1.1 + */ + public Class getSimulationMatrixVectorClass() { + Class result = getOptionAsClass(Option.SIMULATION_MATRIX_VECTOR_CLASS.key); + return result; + } + + /** * Retourne la factory a utilise pour le cache * * @return factory a utilise pour le backend de cache @@ -989,6 +1001,10 @@ 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()), + + // pour les simulations + SIMULATION_MATRIX_VECTOR_CLASS("simulation.matrix.vector.class", n("isisfish.config.simulation.matrix.vector.class.description"), DoubleBigVector.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"), Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-06-17 15:29:15 UTC (rev 4023) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-06-17 15:50:26 UTC (rev 4024) @@ -25,6 +25,8 @@ package fr.ifremer.isisfish.simulator; +import fr.ifremer.isisfish.IsisConfig; +import fr.ifremer.isisfish.IsisFish; import java.io.File; import java.util.HashMap; import java.util.LinkedHashSet; @@ -42,6 +44,7 @@ import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.IsisCache; import fr.ifremer.isisfish.util.Trace; +import org.nuiton.math.matrix.MatrixFactory; /** * Keep all information on one simulation. @@ -101,7 +104,8 @@ }; protected SimulationContext() { - + // force matrix backend for this simulation + MatrixFactory.initMatrixFactoryThreadLocal(IsisFish.config.getSimulationMatrixVectorClass()); } /** Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2014-06-17 15:29:15 UTC (rev 4023) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2014-06-17 15:50:26 UTC (rev 4024) @@ -70,6 +70,7 @@ import fr.ifremer.isisfish.types.Month; import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.CompileHelper; +import org.nuiton.math.matrix.MatrixFactory; /** * Fait une simulation dans la meme jvm. @@ -421,6 +422,10 @@ // Call listener simulation (used per example for prescript) // context.fireBeforeSimulation(); + String matrixBackend = MatrixFactory.getInstance().getVectorClass().getName(); + simulation.getInformation().addInformation("Matrix backend: " + + matrixBackend); + log.info("Matrix backend: " + matrixBackend); simulatorObject.simulate(context); // Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java 2014-06-17 15:29:15 UTC (rev 4023) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java 2014-06-17 15:50:26 UTC (rev 4024) @@ -225,6 +225,7 @@ modelBuilder.addOption(IsisConfig.Option.SIMULATOR_IN_MAXTHREADS); modelBuilder.addOption(IsisConfig.Option.SIMULATOR_SUB_MAXPROCESS); modelBuilder.addOption(IsisConfig.Option.SIMULATOR_SUB_MAXMEMORY); + modelBuilder.addOption(IsisConfig.Option.SIMULATION_MATRIX_VECTOR_CLASS); modelBuilder.addOption(IsisConfig.Option.MAPPED_RESULT_MATRIX_VECTOR_CLASS); // category database vcs

1 0

r4023 - in trunk: . src/main/java/fr/ifremer/isisfish src/main/java/fr/ifremer/isisfish/actions src/main/resources/i18n
by dcosse＠users.forge.codelutin.com June 17, 2014

June 17, 2014

Author: dcosse Date: 2014-06-17 17:29:15 +0200 (Tue, 17 Jun 2014) New Revision: 4023 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4023 Log: mise en place d'un mechanisme de validation des simulations Added: trunk/src/main/java/fr/ifremer/isisfish/actions/ValidateSimulationAction.java Modified: trunk/go.sh trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java trunk/src/main/resources/i18n/isis-fish_en_GB.properties trunk/src/main/resources/i18n/isis-fish_fr_FR.properties Modified: trunk/go.sh =================================================================== --- trunk/go.sh 2014-06-17 14:30:35 UTC (rev 4022) +++ trunk/go.sh 2014-06-17 15:29:15 UTC (rev 4023) @@ -3,7 +3,7 @@ # Java executable JAVA=java -TEMP=`getopt -o dnt:: --long debug,nosuspend,trace:: \ +TEMP=`getopt -o dnt:: --long debug,nosuspend,cheked,trace:: \ -n 'go.sh' -- "$@"` if [ $? != 0 ] ; then @@ -14,26 +14,38 @@ eval set -- "$TEMP" while true ; do - case "$1" in - -d|--debug) - echo "Debug mode" - DEBUG="-server -Xdebug -Xnoagent -Djava.compiler=NONE -Xrunjdwp:transport=dt_socket,address=38000,server=y" - shift ;; - -n|--nosuspend) - echo "Debug no suspend mode" - DEBUG="$DEBUG,suspend=n" - shift ;; - -t|--trace) - echo "Trace mode" - case "$2" in - "") TRACE_FILE="-Daspectwerkz.definition.file=$rep/src/main/resources/trace-aop.xml" # -Daspectwerkz.transform.verbose=true" # -Daspectwerkz.transform.details=true" - ;; - *) TRACE_FILE="-Daspectwerkz.definition.file=$2" # -Daspectwerkz.transform.verbose=true" # -Daspectwerkz.transform.details=true" - esac - shift 2 ;; - --) shift ; break ;; - *) echo "Bad argument $1!" ; exit 1 ;; - esac + case "$1" in + -d|--debug) + echo "Debug mode" + DEBUG="-server -Xdebug -Xnoagent -Djava.compiler=NONE -Xrunjdwp:transport=dt_socket,address=38000,server=y" + shift ;; + -n|--nosuspend) + echo "Debug no suspend mode" + DEBUG="$DEBUG,suspend=n" + shift ;; + -c|--checked) + echo "Checked mode" + CHECK="-server -Djava.compiler=NONE ,address=38000,server=y" + shift ;; + -t|--trace) + echo "Trace mode" + + case "$2" in + "") + TRACE_FILE="-Daspectwerkz.definition.file=$rep/src/main/resources/trace-aop.xml" # -Daspectwerkz.transform.verbose=true" # -Daspectwerkz.transform.details=true" + ;; + *) + TRACE_FILE="-Daspectwerkz.definition.file=$2" # -Daspectwerkz.transform.verbose=true" # -Daspectwerkz.transform.details=true" + esac + + shift 2 ;; + --) + shift ; + break ;; + *) + echo "Bad argument $1!"; + exit 1 ;; + esac done dir=$(dirname $0) @@ -67,6 +79,6 @@ done LOG="-Dlog4j.configuration=file:$rep/src/main/resources/log4j.properties" # -Dlog4j.debug" -echo $JAVA -Xmx$MX -Xms$MX -classpath $CL $NOaspectwerkz $TRACE_FILE $LOG $JVM_OPT $DEBUG fr.ifremer.isisfish.IsisFish "$@" -$JAVA -Xmx$MX -Xms$MX -classpath $CL $NOaspectwerkz $TRACE_FILE $LOG $JVM_OPT $DEBUG fr.ifremer.isisfish.IsisFish "$@" +echo $JAVA -Xmx$MX -Xms$MX -classpath $CL $NOaspectwerkz $TRACE_FILE $LOG $JVM_OPT $DEBUG $CHECK fr.ifremer.isisfish.IsisFish "$@" +$JAVA -Xmx$MX -Xms$MX -classpath $CL $NOaspectwerkz $TRACE_FILE $LOG $JVM_OPT $DEBUG $CHECK fr.ifremer.isisfish.IsisFish "$@" #$JAVA -Xmx$MX -Xms$MX -classpath $CL $NOaspectwerkz $TRACE_FILE $LOG $JVM_OPT $DEBUG fr.ifremer.isisfish.ui.update.Counter "$@" Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-06-17 14:30:35 UTC (rev 4022) +++ trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-06-17 15:29:15 UTC (rev 4023) @@ -40,6 +40,7 @@ import java.util.Locale; import java.util.Map; +import fr.ifremer.isisfish.actions.ValidateSimulationAction; import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.lang3.time.DurationFormatUtils; import org.nuiton.math.matrix.DoubleBigVector; @@ -285,7 +286,7 @@ } /** - * Retourne le repertoire ou sont stockes les informations relatives + * Retourne le repertoire ou sont stockées les informations relatives * aux simulations en cours. * * @return monitoring directory @@ -304,7 +305,7 @@ * Get javadoc directory. * * Create directory if not exists. - * + * * @return javadoc directory */ public File getJavadocDirectory() { @@ -1198,7 +1199,9 @@ SIMULATE_WITH_SIMULATION(n(""), SimulationAction.class.getName() + "#simulateWithSimulation", "--simulateWithSimulation"), SIMULATE_WITH_SIMULATION_AND_SCRIPT(n(""), SimulationAction.class.getName() + "#simulateWithSimulationAndScript", "--simulateWithSimulationAndScript"), SIMULATE_REMOTELLY(n(""), SimulationAction.class.getName() + "#simulateRemotelly", "--simulateRemotelly"), - SIMULATE_REMOTELLY_WITH_PRESCRIPT(n(""), SimulationAction.class.getName() + "#simulateRemotellyWithPreScript", "--simulateRemotellyWithPreScript"); + SIMULATE_REMOTELLY_WITH_PRESCRIPT(n(""), SimulationAction.class.getName() + "#simulateRemotellyWithPreScript", "--simulateRemotellyWithPreScript"), + + VALIDATE_WITH_SIMULATION(n(""), ValidateSimulationAction.class.getName() + "#validateSimulation", "--validate"); protected String description; protected String action; Copied: trunk/src/main/java/fr/ifremer/isisfish/actions/ValidateSimulationAction.java (from rev 4014, trunk/src/main/java/fr/ifremer/isisfish/actions/SimulationAction.java) =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/actions/ValidateSimulationAction.java (rev 0) +++ trunk/src/main/java/fr/ifremer/isisfish/actions/ValidateSimulationAction.java 2014-06-17 15:29:15 UTC (rev 4023) @@ -0,0 +1,180 @@ +/* + * #%L + * IsisFish + * + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2002 - 2014 Ifremer, Code Lutin, Benjamin Poussin, Chatellier Eric + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ + +package fr.ifremer.isisfish.actions; + +import fr.ifremer.isisfish.IsisConfig; +import fr.ifremer.isisfish.IsisFish; +import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.simulator.SimulationControl; +import fr.ifremer.isisfish.simulator.launcher.InProcessSimulatorLauncher; +import fr.ifremer.isisfish.simulator.launcher.SimulationItem; +import fr.ifremer.isisfish.simulator.launcher.SimulationService; +import fr.ifremer.isisfish.simulator.launcher.SimulatorLauncher; +import org.apache.commons.io.FileUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.nuiton.config.ApplicationConfig.Action.Step; +import org.nuiton.math.matrix.MatrixND; + +import java.io.File; +import java.text.SimpleDateFormat; +import java.util.Date; +import java.util.List; + +import static org.nuiton.i18n.I18n.t; + +/** + * Check that there are no regressions. + * Monitor execution. + * + */ +public class ValidateSimulationAction { + + /** to use log facility, just put in your code: log.info("..."); */ + private static Log log = LogFactory.getLog(ValidateSimulationAction.class); + + private static final SimpleDateFormat df = new SimpleDateFormat("dd-MM-yy-HH:mm:ss.SS"); + + protected IsisConfig config = null; + + /** + * results from validated simulation + */ + protected static ResultStorage validatedResultStorage; + + public ValidateSimulationAction(IsisConfig config) { + this.config = config; + } + + + /** + * Launch a simulation + * with simulation params the similutaion at the given path. + * + * @param simulationName name of the simulation reference. + * @throws Exception + */ + @Step(IsisConfig.STEP_AFTER_INIT_VCS) + public static void validateSimulation(String simulationName) + throws Exception { + SimulationStorage simulation = SimulationStorage.getSimulation(simulationName); + validatedResultStorage = simulation.getResultStorage(); + + simulateWithSimulation("Validate-From-" + simulationName + "-" + df.format(new Date()), simulation.createZip()); + } + + /** + * Launch a simulation with specified simulationId and simulation zip. + * + * @param simulationId id de simulation + * @param simulationZip Zip de la simulation + * @throws Exception + */ + @Step(IsisConfig.STEP_AFTER_INIT_VCS) + public static void simulateWithSimulation(String simulationId, File simulationZip) + throws Exception { + // just call with null pre script + validateWithSimulationAndScript(simulationId, simulationZip, null); + } + + /** + * Launch a simulation with specified simulationId, simulationZip + * and simulationPrescript. + * + * @param simulationId id de simulation + * @param simulationZip Zip de la simulation + * @param simulationPrescript simulation prescript + * @throws Exception + */ + @Step(IsisConfig.STEP_AFTER_INIT_VCS) + public static void validateWithSimulationAndScript(String simulationId, File simulationZip, File simulationPrescript) + throws Exception { + + if (log.isInfoEnabled()) { + log.info("Command line action : validateWithSimulationAndScript (" + simulationId + ", " + simulationZip.getAbsolutePath() + ", " + simulationPrescript + ")"); + } + + // ne pas mettre la date, car le sub process la met deja + " " + new SimpleDateFormat("yyyy-MM-dd-HH-mm").format(new Date()); + String name = simulationId; + + //SimulationStorage simulation = launcher.simulate(null, control, simulationZip); + //simulation.getStorage().closeContext(); + String generatedPrescriptContent = null; + if (simulationPrescript != null && simulationPrescript.canRead()) { + generatedPrescriptContent = FileUtils.readFileToString(simulationPrescript); + } + + SimulationControl control = new SimulationControl(name); + control.setAutoSaveState(true); // needed for remote simulation + + SimulationItem item = new SimulationItem(control, null); + item.setSimulationZip(simulationZip); + item.setGeneratedPrescriptContent(generatedPrescriptContent); + + // lancement de la simulation + SimulatorLauncher launcher = new InProcessSimulatorLauncher(); + launcher.simulate(SimulationService.getService(), item); + SimulationStorage simulation = launcher.getSimulationStorage(SimulationService.getService(), control); + + validateResults(simulation.getResultStorage()); + + simulation.getStorage().closeContext(); + + // FIXME integrer ca dans le process normal d'init + IsisFish.quit(); + } + + /** + * Compare result simulation from the validated ones. + * @param newResultStorage + * @throws Exception + */ + public static void validateResults(ResultStorage newResultStorage) throws Exception { + + if (newResultStorage.getResultName().size() == validatedResultStorage.getResultName().size()) { + log.info(t("isisfish.common.ok") + " nombre de résultats obtenus équivalent :" + newResultStorage.getResultName().size() + "/" + validatedResultStorage.getResultName().size()); + } else { + log.error(t("isisfish.common.ko") + " nombre de résultats obtenus différent :" + newResultStorage.getResultName().size() + "/" + validatedResultStorage.getResultName().size()); + } + + List<String> simuNames = validatedResultStorage.getResultName(); + for (String simuName : simuNames) { + MatrixND validatedMatrix = validatedResultStorage.getMatrix(simuName); + MatrixND newMatrix = newResultStorage.getMatrix(simuName); + if (newMatrix == null) { + log.error(t("isisfish.common.ko") + " " + t("isisfish.error.validation.matrixNotComputed", validatedMatrix.getName())); + } else { + if (validatedMatrix.equalsValues(newMatrix)) { + log.info(t("isisfish.common.ok") + " MatrixND:" + validatedMatrix.getName()); + } else { + log.error(t("isisfish.common.ko") + " MatrixND:" + validatedMatrix.getName()); + } + } + } + } + +} Modified: trunk/src/main/resources/i18n/isis-fish_en_GB.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2014-06-17 14:30:35 UTC (rev 4022) +++ trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2014-06-17 15:29:15 UTC (rev 4023) @@ -129,6 +129,7 @@ isisfish.common.gear=Gear isisfish.common.immigration=immigration isisfish.common.info=info +isisfish.common.ko=KO isisfish.common.migration=migration isisfish.common.module=Module isisfish.common.month=month %1$s @@ -406,6 +407,7 @@ isisfish.error.undefined.zone.recruitment=No recrutment's zone defined isisfish.error.undefined.zone.reproduction=No reprodution's zone defined isisfish.error.unsupported.equation.langage=Unsupported language '%1$s' for equation\: %2$s +isisfish.error.validation.matrixNotComputed=matrix not computed %s isisfish.error.wait.simThread=Can't wait SimThread isisfish.error.warning.title=Warning isisfish.error.write.simulation=Can't write information %1$s Modified: trunk/src/main/resources/i18n/isis-fish_fr_FR.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2014-06-17 14:30:35 UTC (rev 4022) +++ trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2014-06-17 15:29:15 UTC (rev 4023) @@ -129,6 +129,7 @@ isisfish.common.gear=Engin isisfish.common.immigration=immigration isisfish.common.info=Info +isisfish.common.ko=KO isisfish.common.migration=migration isisfish.common.module=Module isisfish.common.month=mois %1$s @@ -406,6 +407,7 @@ isisfish.error.undefined.zone.recruitment=il n'y a pas de zone de recrutement de définie isisfish.error.undefined.zone.reproduction=il n'y a pas de zone de reproduction de définie isisfish.error.unsupported.equation.langage=unsupported langage '%1$s' for equation\: %2$s +isisfish.error.validation.matrixNotComputed=matrice non calulée\:%s isisfish.error.wait.simThread=Can't wait SimThread isisfish.error.warning.title=Attention isisfish.error.write.simulation=Can't write information %1$s

1 0

r4022 - trunk/src/main/java/fr/ifremer/isisfish/ui/simulator
by echatellier＠users.forge.codelutin.com June 17, 2014

June 17, 2014

Author: echatellier Date: 2014-06-17 16:30:35 +0200 (Tue, 17 Jun 2014) New Revision: 4022 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4022 Log: fixes #3955: quand recharge ancienne simulation, isis ne garde pas le simulateur associ?\195?\169 Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/AdvancedParamsUI.jaxx trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/OptimizationHandler.java trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/OptimizationUI.jaxx trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/ParamsUI.jaxx trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/PreScriptsUI.jaxx trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/ResultChoiceUI.jaxx Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/AdvancedParamsUI.jaxx =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/AdvancedParamsUI.jaxx 2014-06-17 12:50:25 UTC (rev 4021) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/AdvancedParamsUI.jaxx 2014-06-17 14:30:35 UTC (rev 4022) @@ -55,6 +55,25 @@ } public void refresh() { + fieldSimulAdvParamsSimulatorSelect.setSelectedItem(getContextValue(SimulAction.class).getSimulationParameter().getSimulatorName()); + fieldSimulationStatistique.setSelected(getContextValue(SimulAction.class).getSimulationParameter().getUseStatistic()); + fieldSimulationCache.setSelected(getContextValue(SimulAction.class).getSimulationParameter().getUseCache()); + + fieldSimulAdvParamsSimulLoggerError.setSelected(getContextValue(SimulAction.class).getSimulationParameter().isSimulErrorLevel()); + fieldSimulAdvParamsSimulLoggerWarn.setSelected(getContextValue(SimulAction.class).getSimulationParameter().isSimulWarnLevel()); + fieldSimulAdvParamsSimulLoggerInfo.setSelected(getContextValue(SimulAction.class).getSimulationParameter().isSimulInfoLevel()); + fieldSimulAdvParamsSimulLoggerDebug.setSelected(getContextValue(SimulAction.class).getSimulationParameter().isSimulDebugLevel()); + + fieldSimulAdvParamsScriptLoggerError.setSelected(getContextValue(SimulAction.class).getSimulationParameter().isScriptErrorLevel()); + fieldSimulAdvParamsScriptLoggerWarn.setSelected(getContextValue(SimulAction.class).getSimulationParameter().isScriptWarnLevel()); + fieldSimulAdvParamsScriptLoggerInfo.setSelected(getContextValue(SimulAction.class).getSimulationParameter().isScriptInfoLevel()); + fieldSimulAdvParamsScriptLoggerDebug.setSelected(getContextValue(SimulAction.class).getSimulationParameter().isScriptDebugLevel()); + + fieldSimulAdvParamsLibLoggerError.setSelected(getContextValue(SimulAction.class).getSimulationParameter().isLibErrorLevel()); + fieldSimulAdvParamsLibLoggerWarn.setSelected(getContextValue(SimulAction.class).getSimulationParameter().isLibWarnLevel()); + fieldSimulAdvParamsLibLoggerInfo.setSelected(getContextValue(SimulAction.class).getSimulationParameter().isLibInfoLevel()); + fieldSimulAdvParamsLibLoggerDebug.setSelected(getContextValue(SimulAction.class).getSimulationParameter().isLibDebugLevel()); + setTableTagValues(); } @@ -123,7 +142,8 @@ <JLabel text="isisfish.advancedParams.simulatorUse"/> </cell> <cell columns="4" fill="horizontal"> - <JComboBox id="fieldSimulAdvParamsSimulatorSelect" model='{new DefaultComboBoxModel(getContextValue(SimulAction.class).getSimulatorNames().toArray())}' onActionPerformed='setSimulatorName()'/> + <JComboBox id="fieldSimulAdvParamsSimulatorSelect" model='{new DefaultComboBoxModel(getContextValue(SimulAction.class).getSimulatorNames().toArray())}' + onActionPerformed='setSimulatorName()'/> </cell> </row> <row> Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/OptimizationHandler.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/OptimizationHandler.java 2014-06-17 12:50:25 UTC (rev 4021) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/OptimizationHandler.java 2014-06-17 14:30:35 UTC (rev 4022) @@ -64,14 +64,17 @@ import fr.ifremer.isisfish.ui.sensitivity.SensitivityTabUI; import fr.ifremer.isisfish.ui.widget.editor.FactorEditorListener; - public class OptimizationHandler { private static final Log log = LogFactory.getLog(OptimizationHandler.class); protected FactorEditorListener factorEditorListener; - public void init(OptimizationUI view) { + public void init(final OptimizationUI view) { + + } + + public void refresh(OptimizationUI view) { // get info SimulAction simulAction = view.getContextValue(SimulAction.class); SimulationParameter param = simulAction.getSimulationParameter(); Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/OptimizationUI.jaxx =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/OptimizationUI.jaxx 2014-06-17 12:50:25 UTC (rev 4021) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/OptimizationUI.jaxx 2014-06-17 14:30:35 UTC (rev 4022) @@ -24,17 +24,17 @@ --> <Table> <script><![CDATA[ - /*protected void $afterCompleteSetup() { + protected void $afterCompleteSetup() { handler.init(this); - }*/ + } // application will be refreshed by regionStorage change protected void regionStorageChanged() { - handler.init(this); + //handler.refresh(this); } public void refresh() { - //handler.refresh(this); + handler.refresh(this); } ]]></script> Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/ParamsUI.jaxx =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/ParamsUI.jaxx 2014-06-17 12:50:25 UTC (rev 4021) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/ParamsUI.jaxx 2014-06-17 14:30:35 UTC (rev 4022) @@ -120,7 +120,7 @@ @Override public void run() { simulAction.regionChange(ParamsUI.this, selected); - refresh(); + getParentContainer(SimulUI.class).refresh(); setSensitivityTabRegion(); getParentContainer(WelcomePanelUI.class).setStatusMessage(t("isisfish.message.region.loaded")); } @@ -188,8 +188,10 @@ @Override public void run() { simulAction.loadOldSimulation(selected); - //refresh(); fieldSimulParamsRegion.setSelectedItem(getContextValue(SimulAction.class).getSimulationParameter().getRegionName()); + + getParentContainer(SimulUI.class).refresh(); + // mise a jour des années fieldSimulParamsNbAnnees.setText(String.valueOf(simulAction.getNumberOfYear())); initSimulationParams(); Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/PreScriptsUI.jaxx =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/PreScriptsUI.jaxx 2014-06-17 12:50:25 UTC (rev 4021) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/PreScriptsUI.jaxx 2014-06-17 14:30:35 UTC (rev 4022) @@ -42,7 +42,8 @@ }*/ ]]></script> <org.fife.ui.rtextarea.RTextScrollPane constraints='BorderLayout.CENTER'> - <org.fife.ui.rsyntaxtextarea.RSyntaxTextArea id="fieldSimulPreScript" syntaxEditingStyle="{org.fife.ui.rsyntaxtextarea.SyntaxConstants.SYNTAX_STYLE_JAVA}" /> + <org.fife.ui.rsyntaxtextarea.RSyntaxTextArea id="fieldSimulPreScript" onFocusLost='save()' + syntaxEditingStyle="{org.fife.ui.rsyntaxtextarea.SyntaxConstants.SYNTAX_STYLE_JAVA}" /> </org.fife.ui.rtextarea.RTextScrollPane> <JButton constraints='BorderLayout.SOUTH' text="isisfish.preScript.backParameter" onActionPerformed='getParentContainer(fr.ifremer.isisfish.ui.SimulationUI.class).selectParametersTab()'/> Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/ResultChoiceUI.jaxx =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/ResultChoiceUI.jaxx 2014-06-17 12:50:25 UTC (rev 4021) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/ResultChoiceUI.jaxx 2014-06-17 14:30:35 UTC (rev 4022) @@ -47,10 +47,10 @@ return getContextValue(SimulAction.class); } - protected void setListSimulResultChooseModel(){ + protected void setListSimulResultChooseModel() { - java.util.List<String> availableResults = getSimulAction().getResultNames(); - java.util.List<String> userResults = getSimulAction().getDefaultResultNames(); + List<String> availableResults = getSimulAction().getResultNames(); + List<String> userResults = getSimulAction().getDefaultResultNames(); // userResults = intersection(userResults,availableResult) userResults.retainAll(availableResults);

1 0

r4021 - trunk/src/main/resources/i18n
by echatellier＠users.forge.codelutin.com June 17, 2014

June 17, 2014

Author: echatellier Date: 2014-06-17 14:50:25 +0200 (Tue, 17 Jun 2014) New Revision: 4021 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4021 Log: Update dates Modified: trunk/src/main/resources/i18n/isis-fish_en_GB.properties trunk/src/main/resources/i18n/isis-fish_fr_FR.properties Modified: trunk/src/main/resources/i18n/isis-fish_en_GB.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2014-06-17 12:46:50 UTC (rev 4020) +++ trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2014-06-17 12:50:25 UTC (rev 4021) @@ -89,7 +89,7 @@ directory\ %s\ must\ be\ a\ directory= dlnorm= filter\ loaded\ in\ %1$s\ ms\ \:\ found\ %2$s\ lines.=filter loaded in %1$s ms \: found %2$s lines. -isisfish.about.abouthtmltext=<html><b>ISIS-Fish (%s)</b><br /><br />Copyright IFREMER-MAERHA 2000-2013.<br /><br /><a href\="http\://www.isis-fish.org">http\://www.isis-fish.org</a><br /><br />Please, report any bug you can found.<html> +isisfish.about.abouthtmltext=<html><b>ISIS-Fish (%s)</b><br /><br />Copyright IFREMER-MAERHA 2000-2014.<br /><br /><a href\="http\://www.isis-fish.org">http\://www.isis-fish.org</a><br /><br />Please, report any bug you can found.<html> isisfish.about.licensetext=You can modify and redistribute the program under the conditions of the GNU General Public License (version 2 or later). A copy of the GPL is in the file "LICENSE.txt" provided with ISIS-Fish. All rights reserved. No guarantees are provided for use of this program. isisfish.about.title=About ISIS-Fish... isisfish.advancedParameters.title=Advanced parameters Modified: trunk/src/main/resources/i18n/isis-fish_fr_FR.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2014-06-17 12:46:50 UTC (rev 4020) +++ trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2014-06-17 12:50:25 UTC (rev 4021) @@ -89,7 +89,7 @@ directory\ %s\ must\ be\ a\ directory= dlnorm= filter\ loaded\ in\ %1$s\ ms\ \:\ found\ %2$s\ lines.=filter loaded in %1$s ms \: found %2$s lines. -isisfish.about.abouthtmltext=<html><b>ISIS-Fish (%s)</b><br /><br />Copyright IFREMER-MAERHA 2000-2013.<br /><br /><a href\="http\://www.isis-fish.org">http\://www.isis-fish.org</a><br /><br />Merci de rapporter les bugs.<html> +isisfish.about.abouthtmltext=<html><b>ISIS-Fish (%s)</b><br /><br />Copyright IFREMER-MAERHA 2000-2014.<br /><br /><a href\="http\://www.isis-fish.org">http\://www.isis-fish.org</a><br /><br />Merci de rapporter les bugs.<html> isisfish.about.licensetext=Vous pouvez modifier et redistribuer ce programme sous les conditions énoncées par la licence GNU GPL (version 2 ou ultérieure). Une copie de la licence GPL est dans le fichier « LICENSE.txt » fourni avec ISIS-Fish. Tous droits réservés. Aucune garantie n'est fournie pour l'utilisation de ce programme. isisfish.about.title=À propos de ISIS-Fish... isisfish.advancedParameters.title=Paramètres avancés

1 0

r4020 - trunk/src/main/java/fr/ifremer/isisfish/mexico/xml
by echatellier＠users.forge.codelutin.com June 17, 2014

June 17, 2014

Author: echatellier Date: 2014-06-17 14:46:50 +0200 (Tue, 17 Jun 2014) New Revision: 4020 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4020 Log: fixes #5239: les groupes de facteurs continus se "d?\195?\169groupent" en chargeant une ancienne AS Modified: trunk/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java Modified: trunk/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java 2014-06-17 12:34:23 UTC (rev 4019) +++ trunk/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java 2014-06-17 12:46:50 UTC (rev 4020) @@ -716,7 +716,7 @@ // add factor to existing or new group FactorGroup group = rootGroup; if (StringUtils.isNotBlank(groupName)) { - group = groups.get(group); + group = groups.get(groupName); if (group == null) { group = new FactorGroup(groupName, "continuous".equals(groupType)); groups.put(groupName, group);

1 0

r4019 - in trunk/src/main/java/fr/ifremer/isisfish: simulator/sensitivity simulator/sensitivity/domain ui/sensitivity/wizard
by echatellier＠users.forge.codelutin.com June 17, 2014

June 17, 2014

Author: echatellier Date: 2014-06-17 14:34:23 +0200 (Tue, 17 Jun 2014) New Revision: 4019 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4019 Log: fixes #5245: R?\195?\169introduire la possibilit?\195?\169 de d?\195?\169finir des facteurs continus sur des matrices Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityUtils.java trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/ContinuousDistributionPanel.java trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/SensitivityWizardHandler.java Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityUtils.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityUtils.java 2014-06-17 09:02:25 UTC (rev 4018) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityUtils.java 2014-06-17 12:34:23 UTC (rev 4019) @@ -30,6 +30,7 @@ import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +import org.nuiton.math.matrix.MatrixND; import fr.ifremer.isisfish.entities.Equation; import fr.ifremer.isisfish.types.RangeOfValues; @@ -134,6 +135,8 @@ result = true; } else if (value instanceof Equation) { result = true; + } else if (value instanceof MatrixND) { + result = true; } else if (value instanceof RangeOfValues) { RangeOfValues rangeOfValues = (RangeOfValues)value; if (rangeOfValues.getType().equals("Float")) { Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java 2014-06-17 09:02:25 UTC (rev 4018) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java 2014-06-17 12:34:23 UTC (rev 4019) @@ -35,6 +35,7 @@ import org.apache.commons.beanutils.MethodUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +import org.nuiton.math.matrix.MatrixND; import fr.ifremer.isisfish.IsisFishRuntimeException; import fr.ifremer.isisfish.simulator.sensitivity.Distribution; @@ -178,19 +179,19 @@ args.add(identifier); // build distribution param args list - Class distClass = distribution.getDistClass(); + // QUNIFPC est un cas particulier dans toutes les distributions possibles if (distribution == Distribution.QUNIFPC) { // special management : % to min/max Object reference = distributionParameters.get(Distribution.QUNIFPC.getDistibutionParams()[0].getName()); double coef = (Double)distributionParameters.get(Distribution.QUNIFPC.getDistibutionParams()[1].getName()); - double ref = (Double)reference; - args.add(ref * (1.0 - coef)); // min - args.add(ref * (1.0 + coef)); // max - } else if (distribution == Distribution.QUNIFMM) { - Object min = distributionParameters.get(Distribution.QUNIFMM.getDistibutionParams()[0].getName()); - args.add(min); - Object max = distributionParameters.get(Distribution.QUNIFMM.getDistibutionParams()[1].getName()); - args.add(max); + if (reference instanceof MatrixND) { + args.add(1.0 - coef); // min + args.add(1.0 + coef); // max + } else { + double ref = (Double)reference; + args.add(ref * (1.0 - coef)); // min + args.add(ref * (1.0 + coef)); // max + } } else { for (DistributionParam param : distribution.getDistibutionParams()) { String name = param.getName(); @@ -199,11 +200,13 @@ } } - // add default value for lower.tail = TRUE, log.p = FALSE + // add default value for lower.tail = TRUE args.add(true); + // add default value forlog.p = FALSE args.add(false); // invoke quantile method + Class distClass = distribution.getDistClass(); Object result = null; try { result = MethodUtils.invokeStaticMethod(distClass, "quantile", args.toArray()); @@ -213,6 +216,14 @@ } } + // pour les matrices, on retourne la matrice multipliée par la valeur données par R + if (distribution == Distribution.QUNIFPC) { + Object reference = distributionParameters.get(Distribution.QUNIFPC.getDistibutionParams()[0].getName()); + if (reference instanceof MatrixND) { + MatrixND ref = ((MatrixND)reference).copy(); + result = ref.mults((Double)result); + } + } return result; } Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/ContinuousDistributionPanel.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/ContinuousDistributionPanel.java 2014-06-17 09:02:25 UTC (rev 4018) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/ContinuousDistributionPanel.java 2014-06-17 12:34:23 UTC (rev 4019) @@ -44,6 +44,8 @@ import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +import org.nuiton.math.matrix.MatrixND; +import org.nuiton.math.matrix.gui.MatrixPanelEditor; import fr.ifremer.isisfish.simulator.sensitivity.Distribution; import fr.ifremer.isisfish.simulator.sensitivity.Distribution.DistributionParam; @@ -89,8 +91,16 @@ GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0, 0, 0, 0), 0, 0)); + // values possibility depending on input type + Distribution[] values; + if (originalValue instanceof MatrixND) { + values = new Distribution[]{Distribution.QUNIFPC}; + } else { + values = Distribution.values(); + } + // combobox - distributionCombo = new JComboBox<Distribution>(Distribution.values()); + distributionCombo = new JComboBox<Distribution>(values); // important : for setSelectedItem to fire event distributionCombo.setSelectedItem(null); distributionCombo.addItemListener(this); @@ -128,7 +138,11 @@ if (value != null) { JComponent comp = paramComponents.get(paramComponentIndex); - ((JTextComponent)comp).setText(value.toString()); + if (comp instanceof MatrixPanelEditor) { + ((MatrixPanelEditor)comp).setMatrix((MatrixND)value); + } else { + ((JTextComponent)comp).setText(value.toString()); + } } else { if (log.isWarnEnabled()) { log.warn("Param " + param.getName() + " not found during init"); @@ -180,16 +194,28 @@ JComponent paramField = getParamField(param); paramField.setToolTipText(param.getDescription()); - // rendu simple - dynamicPanel.add(paramLabel, new GridBagConstraints(0, index, 1, 1, 0, 0, - GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, - new Insets(0, 0, 0, 0), 0, 0)); + // rendu étendu pour les matrix panels + if (paramField instanceof MatrixPanelEditor) { + dynamicPanel.add(paramLabel, new GridBagConstraints(0, index, 2, 1, 0, 0, + GridBagConstraints.NORTHWEST, GridBagConstraints.HORIZONTAL, + new Insets(0, 0, 0, 0), 0, 0)); + index++; + dynamicPanel.add(paramField, new GridBagConstraints(0, index, 2, 1, 1, 1, + GridBagConstraints.NORTH, GridBagConstraints.BOTH, + new Insets(0, 0, 0, 0), 0, 0)); + index++; + } else { + // rendu simple + dynamicPanel.add(paramLabel, new GridBagConstraints(0, index, 1, 1, 0, 0, + GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, + new Insets(0, 0, 0, 0), 0, 0)); + + dynamicPanel.add(paramField, new GridBagConstraints(1, index, 1, 1, 1, 0, + GridBagConstraints.NORTH, GridBagConstraints.HORIZONTAL, + new Insets(0, 0, 0, 0), 0, 0)); + index++; + } - dynamicPanel.add(paramField, new GridBagConstraints(1, index, 1, 1, 1, 0, - GridBagConstraints.NORTH, GridBagConstraints.HORIZONTAL, - new Insets(0, 0, 0, 0), 0, 0)); - index++; - paramComponents.add(paramField); } @@ -211,7 +237,12 @@ JComponent result; if (param.isOriginalValue()) { - result = new JTextField(originalValue.toString()); + if (originalValue instanceof MatrixND) { + result = new MatrixPanelEditor(); + ((MatrixPanelEditor)result).setMatrix((MatrixND)originalValue); + } else { + result = new JTextField(originalValue.toString()); + } } else { result = new JTextField(); } @@ -250,9 +281,13 @@ for (DistributionParam param : params) { JComponent comp = paramComponents.get(paramComponentIndex); - // XXX echatellier 20131201 : always double type ? - String strValue = ((JTextComponent)comp).getText().trim(); - domain.addDistributionParam(param.getName(), Double.parseDouble(strValue)); + if (comp instanceof MatrixPanelEditor) { + domain.addDistributionParam(param.getName(), ((MatrixPanelEditor)comp).getMatrix()); + } else { + // XXX echatellier 20131201 : always double type ? + String strValue = ((JTextComponent)comp).getText().trim(); + domain.addDistributionParam(param.getName(), Double.parseDouble(strValue)); + } paramComponentIndex++; } Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/SensitivityWizardHandler.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/SensitivityWizardHandler.java 2014-06-17 09:02:25 UTC (rev 4018) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/SensitivityWizardHandler.java 2014-06-17 12:34:23 UTC (rev 4019) @@ -372,6 +372,9 @@ ui.setBeanProperty(property); ui.setBean(bean); result = ui; + } else if (value instanceof MatrixND) { + MatrixND matrix = (MatrixND)value; + result = new ContinuousDistributionPanel(matrix.clone()); } else if (value instanceof TimeUnit) { TimeUnit timeUnit = (TimeUnit)value; //DefaultContinuousPanelUI ui = new DefaultContinuousPanelUI(); @@ -580,6 +583,9 @@ ui.setBeanProperty(property); ui.setBean(entity); result = ui; + } else if (value instanceof MatrixND) { + MatrixND matrix = (MatrixND)value; + result = new ContinuousDistributionPanel(matrix.clone()); } else if (value instanceof TimeUnit) { TimeUnit timeUnit = (TimeUnit)value; //DefaultContinuousPanelUI ui = new DefaultContinuousPanelUI(); @@ -597,7 +603,24 @@ topiaContext.closeContext(); } else { - if (factorPath.startsWith("parameters.rule.")) { + if (factorPath.startsWith("parameters.population.")) { + // la seule facon d'avoir les parametres ici est d'aller + // les chercher dans les parametres de simulation + Pattern pattern = Pattern.compile("^parameters\\.population\\.(\\w+)(\\.(.+)?)$"); + Matcher matcher = pattern.matcher(factorPath); + if (matcher.matches()) { + String populationName = matcher.group(1); + if (log.isDebugEnabled()) { + log.debug("Loading population : " + populationName); + } + TopiaContext topiaContext = getTopiaContext(factorWizardUI); + Population pop = IsisFishDAOHelper.getPopulationDAO(topiaContext).findByName(populationName); + SimulAction action = factorWizardUI.getContextValue(SimulAction.class); + MatrixND N = action.getSimulationParameter().getNumberOf(pop); + result = new ContinuousDistributionPanel(N.clone()); + topiaContext.closeContext(); + } + } else if (factorPath.startsWith("parameters.rule.")) { Pattern pattern = Pattern.compile("^parameters\\.rule\\.(\\d+)\\.parameter\\.(\\w+)(\\..+)?$"); Matcher matcher = pattern.matcher(factorPath); if (matcher.matches()) {

1 0

r4018 - in trunk/src/main: java/fr/ifremer/isisfish/datastore java/fr/ifremer/isisfish/ui/input resources/i18n
by echatellier＠users.forge.codelutin.com June 17, 2014

June 17, 2014

Author: echatellier Date: 2014-06-17 11:02:25 +0200 (Tue, 17 Jun 2014) New Revision: 4018 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4018 Log: Remove import from v2 Removed: trunk/src/main/java/fr/ifremer/isisfish/datastore/update/ Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/input/InputHandler.java trunk/src/main/java/fr/ifremer/isisfish/ui/input/InputUI.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/ui/input/InputHandler.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/input/InputHandler.java 2014-06-16 16:04:46 UTC (rev 4017) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/input/InputHandler.java 2014-06-17 09:02:25 UTC (rev 4018) @@ -61,7 +61,6 @@ import fr.ifremer.isisfish.datastore.RegionStorage; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.datastore.StorageException; -import fr.ifremer.isisfish.datastore.update.ImportFromV2; import fr.ifremer.isisfish.entities.Cell; import fr.ifremer.isisfish.entities.FisheryRegion; import fr.ifremer.isisfish.entities.Gear; @@ -314,29 +313,6 @@ } /** - * Importer la region depuis un fichier XML de la version 2. - * - * @param inputUI inputUI - */ - public void importV2Region(InputUI inputUI) { - - setStatusMessage(inputUI, t("isisfish.message.import.xml.v2.file"), true); - - try { - File file = FileUtil.getFile(".*.xml$", t("isisfish.message.import.region.xml")); - if (file != null) { - new ImportFromV2(true).importXML(file); - - refreshRegionList(inputUI, null); - } - } catch (Exception eee) { - throw new IsisFishRuntimeException(t("isisfish.error.region.import"), eee); - } - - setStatusMessage(inputUI, t("isisfish.message.import.finished")); - } - - /** * Extract from a simulation the region, and rename it with name given * by user. * Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/input/InputUI.jaxx =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/input/InputUI.jaxx 2014-06-16 16:04:46 UTC (rev 4017) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/input/InputUI.jaxx 2014-06-17 09:02:25 UTC (rev 4018) @@ -32,7 +32,6 @@ <JMenu text="isisfish.common.region"> <JMenuItem text="isisfish.input.menu.importRegion" onActionPerformed="getHandler().importRegion(this)" /> <JMenuItem text="isisfish.input.menu.importRenameRegion" onActionPerformed="getHandler().importRegionAndRename(this)" /> - <JMenuItem text="isisfish.input.menu.importRegionV2" onActionPerformed="getHandler().importV2Region(this)" /> <JMenuItem text="isisfish.input.menu.importRegionSimulation" onActionPerformed="getHandler().importRegionFromSimulation(this)" /> <JMenuItem text="isisfish.input.menu.exportRegion" enabled='{isRegionLoaded()}' onActionPerformed="getHandler().exportRegion(this)" /> <JMenuItem text="isisfish.input.menu.copyRegion" enabled='{isRegionLoaded()}' onActionPerformed="getHandler().copyRegion(this)" /> Modified: trunk/src/main/resources/i18n/isis-fish_en_GB.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2014-06-16 16:04:46 UTC (rev 4017) +++ trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2014-06-17 09:02:25 UTC (rev 4018) @@ -211,6 +211,7 @@ isisfish.config.main.simulation.ssh.pbsbinpath.description=PBS executables (qsub, qdel...) directory isisfish.config.main.simulation.ssh.pbsqsuboptions=Qsub arguments isisfish.config.main.simulation.ssh.pbsqsuboptions.description=Arguments used at qsub job sumbit. Default to '-m n' don't send mail. +isisfish.config.main.simulation.ssh.proxy.command.description= isisfish.config.main.simulation.ssh.server=Simulation server isisfish.config.main.simulation.ssh.server.description=Simulation server address isisfish.config.main.simulation.ssh.tmppath=Server temp directory Modified: trunk/src/main/resources/i18n/isis-fish_fr_FR.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2014-06-16 16:04:46 UTC (rev 4017) +++ trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2014-06-17 09:02:25 UTC (rev 4018) @@ -211,6 +211,7 @@ isisfish.config.main.simulation.ssh.pbsbinpath.description=Emplacement des commandes PBS (qsub, qdel...) sur le serveur isisfish.config.main.simulation.ssh.pbsqsuboptions=Arguments qsub isisfish.config.main.simulation.ssh.pbsqsuboptions.description=Arguments utilisés lors de la soumission des jobs. Par défaut '-m n' pas d'envoi de mails. +isisfish.config.main.simulation.ssh.proxy.command.description= isisfish.config.main.simulation.ssh.server=Serveur de simulation isisfish.config.main.simulation.ssh.server.description=Adresse du serveur de simulation isisfish.config.main.simulation.ssh.tmppath=Dossier temporaire

1 0

r4017 - trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher
by echatellier＠users.forge.codelutin.com June 16, 2014

June 16, 2014

Author: echatellier Date: 2014-06-16 18:04:46 +0200 (Mon, 16 Jun 2014) New Revision: 4017 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4017 Log: fixes #5244: Les plans de simulations continuent alors que la simulation n'a pas encore ?\195?\169t?\195?\169 t?\195?\169l?\195?\169charg?\195?\169es depuis caparmor Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java 2014-06-16 15:21:40 UTC (rev 4016) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java 2014-06-16 16:04:46 UTC (rev 4017) @@ -356,8 +356,7 @@ // make sure user is connected try { getSSHSession(); - } - catch(JSchException e) { + } catch(JSchException e) { throw new RemoteException("Can't connect", e); } @@ -399,7 +398,6 @@ // MD5 + SIMULATION zip file // FIXME echatellier 20140402 check not yet existing md5ControlFile and simulation ended - // simulation result will never be downloaded try { File md5ControlFile = downloadResultsMD5File(sshSession, control.getId()); @@ -434,8 +432,7 @@ // control need to be read before, otherwize, setText // in clearSimulationFiles will erase file :( clearSimulationFiles(sshSession, control); - } - else { + } else { if (log.isWarnEnabled()) { log.warn("Simulation zip download failed"); } @@ -444,8 +441,7 @@ // remove temp file md5ControlFile.delete(); } - } - catch(SSHException e) { + } catch(SSHException e) { if (log.isDebugEnabled()) { log.debug(t("Can't download archive : %s", e.getMessage())); } Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java 2014-06-16 15:21:40 UTC (rev 4016) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java 2014-06-16 16:04:46 UTC (rev 4017) @@ -527,8 +527,7 @@ if (control.isStopSimulationRequest()) { launcher.simulationStopRequest(job); simulationEnded = true; - } - else { + } else { launcher.updateControl(service, control); // by default, Progress = ProgressMax = 0 @@ -536,18 +535,20 @@ // and set by end of // fr.ifremer.isisfish.simulator.launcher.InProcessSimulatorLauncher#localSimulateSameThread(SimulationControl, SimulationStorage) - File simulationRoot = SimulationStorage.getSimulationDirectory(control.getId()); + File localControlFile = SimulationStorage.getSimulationControlFile(control.getId()); // si la simulation n'est pas localement presente, c'est pas fini - if (simulationRoot.isDirectory()) { + // la simulation peut être finie, mais non téléchargées + // en testant le fichier de controle, on s'assure que la simulation est physiquement + // présente en local + if (localControlFile.isFile()) { // cas d'une simulation terminée if (control.getProgress() > 0 && control.getProgress() >= control.getProgressMax()) { simulationEnded = true; - } - else { - + } else { // cas d'une simulation arretee par exception + File simulationRoot = SimulationStorage.getSimulationDirectory(control.getId()); File informationFile = SimulationStorage.getSimulationInformationFile(simulationRoot); SimulationInformation information = new SimulationInformation(informationFile); if (StringUtils.isNotEmpty(information.getException())) {

1 0

r4016 - in trunk/src/main/java/fr/ifremer/isisfish: . simulator/launcher ui/config util/ssh
by echatellier＠users.forge.codelutin.com June 16, 2014

June 16, 2014

Author: echatellier Date: 2014-06-16 17:21:40 +0200 (Mon, 16 Jun 2014) New Revision: 4016 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4016 Log: Support jsch proxy command to allow using caparmor outside ifremer network Added: trunk/src/main/java/fr/ifremer/isisfish/util/ssh/ProxyCommand.java Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigAction.java Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-06-16 11:46:42 UTC (rev 4015) +++ trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-06-16 15:21:40 UTC (rev 4016) @@ -181,7 +181,9 @@ public IsisConfig() { for (Option o : Option.values()) { - setDefaultOption(o.key, o.defaultValue); + if (o.defaultValue != null) { + setDefaultOption(o.key, o.defaultValue); + } } for (Action a : Action.values()) { @@ -666,11 +668,15 @@ setOption(Option.SSH_KEY_FILE.key, sshFile.getAbsolutePath()); } - /*public boolean isUseVCS() { - String value = getOption(Option.VCS_TYPE.key); - boolean result = !VCSNone.TYPE_NONE.equals(value); + /** + * La proxy command a ajouter pour pouvoir contacter le serveur cible. + * + * @return ssh proxy command + */ + public String getSimulatorSshProxyCommand() { + String result = getOption(Option.SIMULATOR_SSH_PROXYCOMMAND.key); return result; - }*/ + } /** * Get launch.ui option value. @@ -1014,6 +1020,8 @@ 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"), + /** Serveur accessible par SSH : la proxy commande a ajouter pour ouvrir la connexion. */ + SIMULATOR_SSH_PROXYCOMMAND("simulation.ssh.proxy.command", n("isisfish.config.main.simulation.ssh.proxy.command.description"), null), /** 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/SSHSimulatorLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java 2014-06-16 11:46:42 UTC (rev 4015) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java 2014-06-16 15:21:40 UTC (rev 4016) @@ -57,6 +57,7 @@ import fr.ifremer.isisfish.simulator.SimulationControl; import fr.ifremer.isisfish.util.ssh.InvalidPassphraseException; import fr.ifremer.isisfish.util.ssh.ProgressMonitor; +import fr.ifremer.isisfish.util.ssh.ProxyCommand; import fr.ifremer.isisfish.util.ssh.SSHAgent; import fr.ifremer.isisfish.util.ssh.SSHException; import fr.ifremer.isisfish.util.ssh.SSHUserInfo; @@ -301,7 +302,7 @@ sshSession, control.getId(), simulationPrescript); // start simulation if necessary (multi jobs) ... - startSimulation(simulationItem, simulationid, simulationRemotePath, remoteResultZip, simulationPreScriptPath); + startSimulation(sshSession, simulationItem, simulationid, simulationRemotePath, remoteResultZip, simulationPreScriptPath); } catch (Exception e) { if (log.isErrorEnabled()) { @@ -565,6 +566,12 @@ Session session = jsch.getSession(username, host, port); + // add proxy command if specified + String proxyCommand = IsisFish.config.getSimulatorSshProxyCommand(); + if (StringUtils.isNotBlank(proxyCommand)) { + session.setProxy(new ProxyCommand(proxyCommand)); + } + // username and password will be given via UserInfo interface. SSHUserInfo ui = new SSHUserInfo(); if (sshKeyUsed) { @@ -987,6 +994,7 @@ * * Current simulation can be started later with a PBS multi job. * + * @param session ssh session * @param simulationItem simulation item (needed for additionnal info, simulation, number, indenpendant, etc...) * @param simulationid simulation id * @param simulationRemoteZipPath simulation preparation (input) zip path @@ -995,7 +1003,7 @@ * * @throws Exception */ - protected void startSimulation(SimulationItem simulationItem, String simulationid, String simulationRemoteZipPath, String remoteResultZip, String simulationPreScriptPath) throws Exception { + protected void startSimulation(Session session, SimulationItem simulationItem, String simulationid, String simulationRemoteZipPath, String remoteResultZip, String simulationPreScriptPath) throws Exception { // standalone simulation // no question, generate script, launch it each time @@ -1003,12 +1011,12 @@ // single simulation File simulationPSBScript = getLaunchSimulationScriptFile(simulationid, simulationRemoteZipPath, true, remoteResultZip, simulationPreScriptPath, false); - String scriptRemotePath = uploadSimulationScript(sshSession, simulationid, simulationPSBScript); + String scriptRemotePath = uploadSimulationScript(session, simulationid, simulationPSBScript); // prescript uploaded, delete simulationPSBScript.delete(); - sendStartSimulationRequest(sshSession, simulationid, scriptRemotePath, -1); + sendStartSimulationRequest(session, simulationid, scriptRemotePath, -1); } else { // standalone, on do it for last simulation @@ -1022,13 +1030,13 @@ // multiples jobs simulation File simulationPSBScript = getLaunchSimulationScriptFile(shortSimulationId, simulationRemoteZipPath, simulationItem.isStandaloneSimulationZip(), remoteResultZip, simulationPreScriptPath, true); - String scriptRemotePath = uploadSimulationScript(sshSession, shortSimulationId, simulationPSBScript); + String scriptRemotePath = uploadSimulationScript(session, shortSimulationId, simulationPSBScript); // prescript uploaded, delete simulationPSBScript.delete(); // file will be named with shortSimulationId (instead of simulationId) - sendStartSimulationRequest(sshSession, shortSimulationId, scriptRemotePath, simulationItem.getSimulationNumber()); + sendStartSimulationRequest(session, shortSimulationId, scriptRemotePath, simulationItem.getSimulationNumber()); } else { if (log.isDebugEnabled()) { Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigAction.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigAction.java 2014-06-16 11:46:42 UTC (rev 4015) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/config/SSHLauncherConfigAction.java 2014-06-16 15:21:40 UTC (rev 4016) @@ -47,6 +47,7 @@ import fr.ifremer.isisfish.IsisFish; import fr.ifremer.isisfish.util.ssh.InvalidPassphraseException; +import fr.ifremer.isisfish.util.ssh.ProxyCommand; import fr.ifremer.isisfish.util.ssh.SSHAgent; import fr.ifremer.isisfish.util.ssh.SSHException; import fr.ifremer.isisfish.util.ssh.SSHUserInfo; @@ -287,6 +288,10 @@ } Session session = jsch.getSession(currentSSHUsername, host, port); + String proxyCommand = IsisFish.config.getSimulatorSshProxyCommand(); + if (StringUtils.isNotBlank(proxyCommand)) { + session.setProxy(new ProxyCommand(proxyCommand)); + } // username and password will be given via UserInfo interface. SSHUserInfo ui = new SSHUserInfo(); @@ -441,7 +446,11 @@ } Session session = jsch.getSession(currentSSHUsername, host, port); - + String proxyCommand = IsisFish.config.getSimulatorSshProxyCommand(); + if (StringUtils.isNotBlank(proxyCommand)) { + session.setProxy(new ProxyCommand(proxyCommand)); + } + // username and password will be given via UserInfo interface. SSHUserInfo ui = new SSHUserInfo(); if (sshKeyUsed) { Added: trunk/src/main/java/fr/ifremer/isisfish/util/ssh/ProxyCommand.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/ssh/ProxyCommand.java (rev 0) +++ trunk/src/main/java/fr/ifremer/isisfish/util/ssh/ProxyCommand.java 2014-06-16 15:21:40 UTC (rev 4016) @@ -0,0 +1,84 @@ +/* + * #%L + * IsisFish + * + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2014 Ifremer, Code Lutin, Chatellier Eric + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ + +package fr.ifremer.isisfish.util.ssh; + +import java.io.IOException; +import java.io.InputStream; +import java.io.OutputStream; +import java.net.Socket; + +import com.jcraft.jsch.Proxy; +import com.jcraft.jsch.SocketFactory; + +/** + * Implementation du proxy commande pour pouvoir utiliser un proxy local dans le + * but de faire un rebond à travers un serveur intermédiaire. + * + * @author Eric Chatellier + */ +public class ProxyCommand implements Proxy { + protected String command; + protected Process p = null; + protected InputStream in = null; + protected OutputStream out = null; + + public ProxyCommand(String command) { + this.command = command; + } + + public void connect(SocketFactory socket_factory, String host, int port, int timeout) throws Exception { + String fullCommand = command.replace("%h", host); + fullCommand = fullCommand.replace("%p", new Integer(port).toString()); + p = Runtime.getRuntime().exec(fullCommand); + in = p.getInputStream(); + out = p.getOutputStream(); + } + + public Socket getSocket() { + return null; + } + + public InputStream getInputStream() { + return in; + } + + public OutputStream getOutputStream() { + return out; + } + + public void close() { + try { + if (p != null) { + p.getErrorStream().close(); + p.getOutputStream().close(); + p.getInputStream().close(); + p.destroy(); + p = null; + } + } catch (IOException e) { + } + } +} Property changes on: trunk/src/main/java/fr/ifremer/isisfish/util/ssh/ProxyCommand.java ___________________________________________________________________ Added: svn:eol-style + native Added: svn:keywords + Author Date Id Revision HeadURL

1 0

r4015 - in trunk: . src/main/java/fr/ifremer/isisfish
by echatellier＠users.forge.codelutin.com June 16, 2014

June 16, 2014

Author: echatellier Date: 2014-06-16 13:46:42 +0200 (Mon, 16 Jun 2014) New Revision: 4015 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4015 Log: Update libs Modified: trunk/pom.xml trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-06-12 10:49:10 UTC (rev 4014) +++ trunk/pom.xml 2014-06-16 11:46:42 UTC (rev 4015) @@ -20,7 +20,7 @@ <dependency> <groupId>org.nuiton</groupId> <artifactId>nuiton-utils</artifactId> - <version>3.0-rc-2</version> + <version>3.0-rc-3</version> <scope>compile</scope> </dependency> @@ -111,15 +111,14 @@ <artifactId>mail</artifactId> <version>1.4.7</version> <scope>compile</scope> + <exclusions> + <exclusion> + <artifactId>activation</artifactId> + <groupId>javax.activation</groupId> + </exclusion> + </exclusions> </dependency> - <dependency> - <groupId>javax.activation</groupId> - <artifactId>activation</artifactId> - <version>1.1.1</version> - <scope>compile</scope> - </dependency> -  <dependency> <groupId>org.nuiton.jaxx</groupId> @@ -198,6 +197,12 @@ <groupId>org.apache.commons</groupId> <artifactId>commons-email</artifactId> <version>1.3.2</version> + <exclusions> + <exclusion> + <artifactId>activation</artifactId> + <groupId>javax.activation</groupId> + </exclusion> + </exclusions> </dependency> <dependency> @@ -469,7 +474,7 @@ <signatureVersion>1.0</signatureVersion>  - <jaxxVersion>2.8.5</jaxxVersion> + <jaxxVersion>2.8.7</jaxxVersion> <eugeneVersion>2.7.4</eugeneVersion> <topiaVersion>2.9-rc-1</topiaVersion> <hibernateVersion>4.3.5.Final</hibernateVersion> Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-06-12 10:49:10 UTC (rev 4014) +++ trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-06-16 11:46:42 UTC (rev 4015) @@ -120,7 +120,7 @@ * migration de donnees demande automatiquement un changement de version * d'application. */ - protected final static Version version = new Version(4, 3, 0, 1); + protected final static Version version = new Version(4, 3, 0, 2); protected final static Version majorVersion = new Version(version.getNumber(0)); protected final static Version databaseVersion = new Version(

1 0

r4014 - trunk/src/main/java/fr/ifremer/isisfish/simulator
by echatellier＠users.forge.codelutin.com June 12, 2014

June 12, 2014

Author: echatellier Date: 2014-06-12 12:49:10 +0200 (Thu, 12 Jun 2014) New Revision: 4014 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4014 Log: Escape (again) factor name for equations Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-06-10 17:15:10 UTC (rev 4013) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-06-12 10:49:10 UTC (rev 4014) @@ -376,7 +376,13 @@ * @param value value */ public void setComputeValue(String key, Double value) { - contextEquationValue.put(key, value); + + // on echappe (encore) le nom du facteur, car pour une raison ou pour une autre, + // l'echapement de la méthode fr.ifremer.isisfish.simulator.launcher.SimulationService.fillDesignPlanNominalValue(TopiaContext, DesignPlan) + // n'a pas l'air de suffir pour les equations :( + + String localKey = SensitivityUtils.espaceFactorName(key); + contextEquationValue.put(localKey, value); } /**

1 0

[ANN] - IsisFish 4.3.0.1 released
by codelutin.com Release Notification June 10, 2014

June 10, 2014

The IsisFish team is pleased to announce the isis-fish-4.3.0.1 release! Simulateur de pecherie complexe. Documentation of the project can be found here: http://doc.codelutin.com/isis-fish Changes ------- Changes in this version include: Fixed Bugs: o Update to nuiton-matrix- 2.4.1 Issue: 5198. Thanks to Eric Chatellier. Resolved by echatellier. o Can't run sensitivity analysis since 4.3.0.0 Issue: 5197. Thanks to Eric Chatellier. Resolved by echatellier. Downloads --------- For a manual installation, you can download files here: http://forge.codelutin.com/projects/isis-fish/files * isis-fish-4.3.0.1-bin.zip - http://forge.codelutin.com/attachments/download/1914 Maven artifacts --------------- Artifacts are deployed in nuiton maven repository http://maven.nuiton.org/other-releases/ Have fun! -IsisFish team

1 0

r4013 - trunk
by echatellier＠users.forge.codelutin.com June 10, 2014

June 10, 2014

Author: echatellier Date: 2014-06-10 19:15:10 +0200 (Tue, 10 Jun 2014) New Revision: 4013 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4013 Log: [maven-release-plugin] prepare for next development iteration Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-06-10 17:15:05 UTC (rev 4012) +++ trunk/pom.xml 2014-06-10 17:15:10 UTC (rev 4013) @@ -11,7 +11,7 @@ <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.3.0.1</version> + <version>4.3.0.2-SNAPSHOT</version>  <dependencies> @@ -667,9 +667,9 @@   <scm> - <connection>scm:svn:https://svn.codelutin.com/isis-fish/tags/isis-fish-4.3.0.1</connection> - <developerConnection>scm:svn:https://svn.codelutin.com/isis-fish/tags/isis-fish-4.3.0.1</developerConnection> - <url>https://svn.codelutin.com/isis-fish/tags/isis-fish-4.3.0.1</url> + <connection>scm:svn:https://svn.codelutin.com/isis-fish/trunk</connection> + <developerConnection>scm:svn:https://svn.codelutin.com/isis-fish/trunk</developerConnection> + <url>https://svn.codelutin.com/isis-fish/trunk</url> </scm> <repositories>

1 0

r4012 - in tags: . isis-fish-4.3.0.1
by echatellier＠users.forge.codelutin.com June 10, 2014

June 10, 2014

Author: echatellier Date: 2014-06-10 19:15:05 +0200 (Tue, 10 Jun 2014) New Revision: 4012 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4012 Log: [maven-release-plugin] copy for tag isis-fish-4.3.0.1 Added: tags/isis-fish-4.3.0.1/ Property changes on: tags/isis-fish-4.3.0.1 ___________________________________________________________________ Added: svn:mergeinfo + /branches/4.0.0-svnkit:3665-3698 /branches/4.0.1:3616-3968 /branches/4.1:3601-3670 Added: svn:ignore + maven.log target velocity.log .classpath .project isis-fish.ipr isis-fish.iws isis-fish.iml .settings bin nbproject Inputs_Langoustine .idea

1 0

r4011 - trunk
by echatellier＠users.forge.codelutin.com June 10, 2014

June 10, 2014

Author: echatellier Date: 2014-06-10 19:14:56 +0200 (Tue, 10 Jun 2014) New Revision: 4011 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4011 Log: [maven-release-plugin] prepare release isis-fish-4.3.0.1 Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-06-10 17:08:58 UTC (rev 4010) +++ trunk/pom.xml 2014-06-10 17:14:56 UTC (rev 4011) @@ -11,7 +11,7 @@ <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.3.0.1-SNAPSHOT</version> + <version>4.3.0.1</version>  <dependencies> @@ -667,9 +667,9 @@   <scm> - <connection>scm:svn:https://svn.codelutin.com/isis-fish/trunk</connection> - <developerConnection>scm:svn:https://svn.codelutin.com/isis-fish/trunk</developerConnection> - <url>https://svn.codelutin.com/isis-fish/trunk</url> + <connection>scm:svn:https://svn.codelutin.com/isis-fish/tags/isis-fish-4.3.0.1</connection> + <developerConnection>scm:svn:https://svn.codelutin.com/isis-fish/tags/isis-fish-4.3.0.1</developerConnection> + <url>https://svn.codelutin.com/isis-fish/tags/isis-fish-4.3.0.1</url> </scm> <repositories>

1 0

r4010 - trunk
by echatellier＠users.forge.codelutin.com June 10, 2014

June 10, 2014

Author: echatellier Date: 2014-06-10 19:08:58 +0200 (Tue, 10 Jun 2014) New Revision: 4010 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4010 Log: Fix build Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-06-10 17:08:04 UTC (rev 4009) +++ trunk/pom.xml 2014-06-10 17:08:58 UTC (rev 4010) @@ -11,7 +11,7 @@ <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.3.0.1</version> + <version>4.3.0.1-SNAPSHOT</version>  <dependencies> @@ -667,9 +667,9 @@   <scm> - <connection>scm:svn:https://svn.codelutin.com/isis-fish/tags/isis-fish-4.3.0.1</connection> - <developerConnection>scm:svn:https://svn.codelutin.com/isis-fish/tags/isis-fish-4.3.0.1</developerConnection> - <url>https://svn.codelutin.com/isis-fish/tags/isis-fish-4.3.0.1</url> + <connection>scm:svn:https://svn.codelutin.com/isis-fish/trunk</connection> + <developerConnection>scm:svn:https://svn.codelutin.com/isis-fish/trunk</developerConnection> + <url>https://svn.codelutin.com/isis-fish/trunk</url> </scm> <repositories>

1 0

r4009 - trunk/src/test/java/fr/ifremer/isisfish/mexico
by echatellier＠users.forge.codelutin.com June 10, 2014

June 10, 2014

Author: echatellier Date: 2014-06-10 19:08:04 +0200 (Tue, 10 Jun 2014) New Revision: 4009 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4009 Log: Disable failing test Modified: trunk/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java Modified: trunk/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java =================================================================== --- trunk/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java 2014-06-10 17:05:27 UTC (rev 4008) +++ trunk/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java 2014-06-10 17:08:04 UTC (rev 4009) @@ -439,9 +439,13 @@ * * @throws IOException * @throws IsisFishException - * @throws TopiaException + * @throws TopiaException + * + * This test may fail because of testPercentageMinMaxFactor(fr.ifremer.isisfish.mexico.MexicoHelperTest) Time elapsed: 0.528 sec <<< FAILURE! + * org.junit.ComparisonFailure: expected:<...="Tue Jun 10 18:54:3[5] CEST 2014" id=""> + * ...> but was:<...="Tue Jun 10 18:54:3[6] CEST 2014" id=""> */ - @Test + //@Test public void testPercentageMinMaxFactor() throws IOException, IsisFishException, TopiaException { // get test plan and add some STRANGES factors

1 0

r4008 - trunk
by maven-release＠users.forge.codelutin.com June 10, 2014

June 10, 2014

Author: maven-release Date: 2014-06-10 19:05:27 +0200 (Tue, 10 Jun 2014) New Revision: 4008 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4008 Log: [maven-release-plugin] prepare release isis-fish-4.3.0.1 Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-06-10 16:45:59 UTC (rev 4007) +++ trunk/pom.xml 2014-06-10 17:05:27 UTC (rev 4008) @@ -11,7 +11,7 @@ <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.3.0.1-SNAPSHOT</version> + <version>4.3.0.1</version>  <dependencies> @@ -667,9 +667,9 @@   <scm> - <connection>scm:svn:https://svn.codelutin.com/isis-fish/trunk</connection> - <developerConnection>scm:svn:https://svn.codelutin.com/isis-fish/trunk</developerConnection> - <url>https://svn.codelutin.com/isis-fish/trunk</url> + <connection>scm:svn:https://svn.codelutin.com/isis-fish/tags/isis-fish-4.3.0.1</connection> + <developerConnection>scm:svn:https://svn.codelutin.com/isis-fish/tags/isis-fish-4.3.0.1</developerConnection> + <url>https://svn.codelutin.com/isis-fish/tags/isis-fish-4.3.0.1</url> </scm> <repositories>

1 0

r4007 - in trunk: . src/main/java/fr/ifremer/isisfish/actions src/main/java/fr/ifremer/isisfish/simulator src/main/java/fr/ifremer/isisfish/simulator/launcher src/main/java/fr/ifremer/isisfish/simulator/sensitivity
by echatellier＠users.forge.codelutin.com June 10, 2014

June 10, 2014

Author: echatellier Date: 2014-06-10 18:45:59 +0200 (Tue, 10 Jun 2014) New Revision: 4007 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4007 Log: fixes #5197: Can't run sensitivity analysis since 4.3.0.0 fixes #5198: Update to nuiton-matrix-2.4.1 Modified: trunk/pom.xml trunk/src/main/java/fr/ifremer/isisfish/actions/SimulationAction.java trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationPreScriptListener.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/SimulationItem.java trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SubProcessSimulationLauncher.java trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/FactorHelper.java Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-06-06 06:16:21 UTC (rev 4006) +++ trunk/pom.xml 2014-06-10 16:45:59 UTC (rev 4007) @@ -6,7 +6,7 @@ <parent> <groupId>org.nuiton</groupId> <artifactId>mavenpom4redmine</artifactId> - <version>5.0.8</version> + <version>5.0.9</version> </parent> <groupId>fr.ifremer</groupId> @@ -81,14 +81,14 @@ <dependency> <groupId>org.nuiton.matrix</groupId> <artifactId>nuiton-matrix</artifactId> - <version>2.4</version> + <version>2.4.1</version> <scope>compile</scope> </dependency> <dependency> <groupId>org.nuiton.matrix</groupId> <artifactId>nuiton-matrix-gui</artifactId> - <version>2.4</version> + <version>2.4.1</version> <scope>compile</scope> </dependency> Modified: trunk/src/main/java/fr/ifremer/isisfish/actions/SimulationAction.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/actions/SimulationAction.java 2014-06-06 06:16:21 UTC (rev 4006) +++ trunk/src/main/java/fr/ifremer/isisfish/actions/SimulationAction.java 2014-06-10 16:45:59 UTC (rev 4007) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2002 - 2012 Ifremer, Code Lutin, Benjamin Poussin, Chatellier Eric + * Copyright (C) 2002 - 2014 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 @@ -82,8 +82,7 @@ FileInputStream inStream = new FileInputStream(parameterFile); try { props.load(inStream); - } - finally { + } finally { inStream.close(); } @@ -142,9 +141,9 @@ //SimulationStorage simulation = launcher.simulate(null, control, simulationZip); //simulation.getStorage().closeContext(); - String simulationPrescriptContent = null; + String generatedPrescriptContent = null; if (simulationPrescript != null && simulationPrescript.canRead()) { - simulationPrescriptContent = FileUtils.readFileToString(simulationPrescript); + generatedPrescriptContent = FileUtils.readFileToString(simulationPrescript); } SimulationControl control = new SimulationControl(name); @@ -152,7 +151,7 @@ SimulationItem item = new SimulationItem(control, null); item.setSimulationZip(simulationZip); - item.setSimulationPrescriptContent(simulationPrescriptContent); + item.setGeneratedPrescriptContent(generatedPrescriptContent); // lancement de la simulation SimulatorLauncher launcher = new InProcessSimulatorLauncher(); @@ -222,9 +221,9 @@ //SimulationStorage simulation = launcher.simulate(null, control, simulationZip); //simulation.getStorage().closeContext(); - String simulationPrescriptContent = null; + String generatedPrescriptContent = null; if (simulationPrescript != null && simulationPrescript.canRead()) { - simulationPrescriptContent = FileUtils.readFileToString(simulationPrescript); + generatedPrescriptContent = FileUtils.readFileToString(simulationPrescript); } SimulationControl control = new SimulationControl(name); @@ -232,7 +231,7 @@ SimulationItem item = new SimulationItem(control, null); item.setSimulationZip(simulationZip); - item.setSimulationPrescriptContent(simulationPrescriptContent); + item.setGeneratedPrescriptContent(generatedPrescriptContent); // lancement de la simulation SimulatorLauncher launcher = new InProcessSimulatorLauncher(); Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationPreScriptListener.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationPreScriptListener.java 2014-06-06 06:16:21 UTC (rev 4006) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationPreScriptListener.java 2014-06-10 16:45:59 UTC (rev 4007) @@ -76,18 +76,14 @@ // utilisation de la db en memoire que l'on commitera TopiaContext tx = context.getDB(); - Map<String, Object> args = new HashMap<>(); - args.put("context", context); - args.put("db", tx); - if (StringUtils.isNotBlank(generatedPreScript)) { EvaluatorHelper.evaluate(SimulationPreScript.class.getPackage().getName(), - "GeneratedPreScript", SimulationPreScript.class, generatedPreScript, args); + "GeneratedPreScript", SimulationPreScript.class, generatedPreScript, context, tx); } if (parameters.getUsePreScript() && StringUtils.isNotBlank(presimulationScript)) { EvaluatorHelper.evaluate(SimulationPreScript.class.getPackage().getName(), - "PreScript", SimulationPreScript.class, presimulationScript, args); + "PreScript", SimulationPreScript.class, presimulationScript, context, tx); } tx.commitTransaction(); Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2014-06-06 06:16:21 UTC (rev 4006) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2014-06-10 16:45:59 UTC (rev 4007) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2002 - 2012 Ifremer, Code Lutin, Benjamin Poussin, Chatellier Eric + * Copyright (C) 2002 - 2014 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 @@ -28,12 +28,10 @@ import static org.nuiton.i18n.I18n.t; import java.io.File; -import java.net.MalformedURLException; import java.net.URL; import java.rmi.RemoteException; import java.text.SimpleDateFormat; import java.util.ArrayList; -import java.util.Arrays; import java.util.Enumeration; import java.util.List; @@ -99,7 +97,7 @@ // get real simulation informations for this launcher SimulationControl control = simulationItem.getControl(); File simulationZip = simulationItem.getSimulationZip(); - String simulationPrescript = simulationItem.getSimulationPrescriptContent(); + String generatedPrescript = simulationItem.getGeneratedPrescriptContent(); String id = control.getId(); if (log.isInfoEnabled()) { @@ -129,18 +127,17 @@ if (log.isDebugEnabled()) { log.debug("Timing : after import zip : " + new java.util.Date()); } - + // WARNING: make sure to not open Region before being in simulation context // add missing control informations SimulationParameter param = simulation.getParameter(); control.setStep(new TimeStep()); control.setProgress(0); control.setStarted(true); - + // replace prescript if specified on method - if (StringUtils.isNotBlank(simulationPrescript)) { - param.setUsePreScript(true); - param.setPreScript(simulationPrescript); + if (StringUtils.isNotBlank(generatedPrescript)) { + param.setGeneratedPreScript(generatedPrescript); } int lastYear = param.getNumberOfYear(); Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java 2014-06-06 06:16:21 UTC (rev 4006) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SSHSimulatorLauncher.java 2014-06-10 16:45:59 UTC (rev 4007) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2008 - 2010 Ifremer, Code Lutin, Chatellier Eric + * Copyright (C) 2008 - 2014 Ifremer, Code Lutin, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -272,7 +272,7 @@ // get simulation information for this launcher SimulationControl control = simulationItem.getControl(); File simulationZip = simulationItem.getSimulationZip(); - String simulationPrescript = simulationItem.getSimulationPrescriptContent(); + String simulationPrescript = simulationItem.getGeneratedPrescriptContent(); // check username if (StringUtils.isBlank(IsisFish.config.getSimulatorSshUsername())) { Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationItem.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationItem.java 2014-06-06 06:16:21 UTC (rev 4006) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationItem.java 2014-06-10 16:45:59 UTC (rev 4007) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2002 - 2010 Ifremer, Code Lutin, Benjamin Poussin + * Copyright (C) 2002 - 2014 Ifremer, Code Lutin, Benjamin Poussin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -80,7 +80,7 @@ protected boolean standaloneSimulationZip = true; /** Simulation prescript. */ - protected String simulationPrescriptContent; + protected String generatedPrescriptContent; /** * La simulation doit être lancée seule, sinon les simulations sont @@ -174,22 +174,18 @@ /** * Get simulation prescript. * - * @return the simulationPrescriptPath - * - * @deprecated use cached simulation parameter instead + * @return the generatedPrescriptContent */ - public String getSimulationPrescriptContent() { - - String preScript = simulationPrescriptContent; - + public String getGeneratedPrescriptContent() { + + String preScript = generatedPrescriptContent; + // simulationPrescriptContent is not null when isis is lauched with // simulation on comand line // If preScript but params is not null, simulation has been launched by // UI, use cached simulation parameters if (preScript == null && parameter != null) { - if (parameter.getUsePreScript()) { - preScript = parameter.getPreScript(); - } + preScript = parameter.getGeneratedPreScript(); } return preScript; @@ -198,12 +194,10 @@ /** * Set simulation prescript. * - * @param simulationPrescriptContent the simulationPrescriptContent to set - * - * @deprecated use cached simulation parameter instead + * @param generatedPrescriptContent the generatedPrescriptContent to set */ - public void setSimulationPrescriptContent(String simulationPrescriptContent) { - this.simulationPrescriptContent = simulationPrescriptContent; + public void setGeneratedPrescriptContent(String generatedPrescriptContent) { + this.generatedPrescriptContent = generatedPrescriptContent; } /** Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SubProcessSimulationLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SubProcessSimulationLauncher.java 2014-06-06 06:16:21 UTC (rev 4006) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SubProcessSimulationLauncher.java 2014-06-10 16:45:59 UTC (rev 4007) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2002 - 2011 Ifremer, Code Lutin, Benjamin Poussin, Chatellier Eric + * Copyright (C) 2002 - 2014 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 @@ // get simulation information for this launcher SimulationControl control = simulationItem.getControl(); File simulationZip = simulationItem.getSimulationZip(); - String simulationPrescript = simulationItem.getSimulationPrescriptContent(); + String simulationPrescript = simulationItem.getGeneratedPrescriptContent(); String simulationId = control.getId(); SimulationStorage simulation = null; Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/FactorHelper.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/FactorHelper.java 2014-06-06 06:16:21 UTC (rev 4006) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/FactorHelper.java 2014-06-10 16:45:59 UTC (rev 4007) @@ -22,11 +22,6 @@ * #L% */ - -import fr.ifremer.isisfish.rule.Rule; -import fr.ifremer.isisfish.rule.RuleHelper; -import fr.ifremer.isisfish.simulator.sensitivity.domain.EquationDiscreteDomain; -import fr.ifremer.isisfish.util.ConverterUtil; import java.util.ArrayList; import java.util.Collection; import java.util.List; @@ -34,13 +29,20 @@ import java.util.concurrent.atomic.AtomicInteger; import java.util.regex.Matcher; import java.util.regex.Pattern; + import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.beanutils.ConvertUtilsBean; import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.nuiton.math.matrix.MatrixND; +import org.nuiton.topia.persistence.TopiaEntity; +import fr.ifremer.isisfish.rule.Rule; +import fr.ifremer.isisfish.rule.RuleHelper; +import fr.ifremer.isisfish.simulator.sensitivity.domain.EquationDiscreteDomain; +import fr.ifremer.isisfish.util.ConverterUtil; + /** * Useful method for factor * - create prescript with factor list @@ -75,6 +77,7 @@ buffer.append("import org.apache.commons.beanutils.ConvertUtilsBean;\n"); buffer.append("import fr.ifremer.isisfish.util.ConverterUtil;\n"); buffer.append("import fr.ifremer.isisfish.simulator.SimulationParameter;\n"); + buffer.append("import org.nuiton.topia.persistence.TopiaEntity;\n"); buffer.append("ConvertUtilsBean beanUtils = ConverterUtil.getConverter(db);\n"); buffer.append("SimulationParameter params = context.getSimulationStorage().getParameter();\n"); generatePreScript(beanUtils, buffer, new AtomicInteger(), factors); @@ -163,9 +166,9 @@ String path = factor.getPath(); String topiaId = path.substring(0, path.lastIndexOf('#')); String property = path.substring(path.lastIndexOf('#') + 1); - // Double value123 = beanUtils.convert("mystringvalue", Double.class); + // Double value123 = (Double)beanUtils.convert("mystringvalue", Double.class); buffer.append(value.getClass().getName()).append(" value"); - buffer.append(factorIndex).append(" = beanUtils.convert(\""); + buffer.append(factorIndex).append(" = (").append(value.getClass().getName()).append(")beanUtils.convert(\""); buffer.append(escValue).append("\", ").append(value.getClass().getName()); buffer.append(".class);\n"); // TopiaEntity entity123 = db.findByTopiaId(topiaId);

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r4006 - trunk/src/main/java/fr/ifremer/isisfish
by echatellier＠users.forge.codelutin.com June 6, 2014

June 6, 2014

Author: echatellier Date: 2014-06-06 08:16:21 +0200 (Fri, 06 Jun 2014) New Revision: 4006 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4006 Log: Update versions Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-06-02 14:57:50 UTC (rev 4005) +++ trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-06-06 06:16:21 UTC (rev 4006) @@ -120,7 +120,7 @@ * migration de donnees demande automatiquement un changement de version * d'application. */ - protected final static Version version = new Version(4, 3, 0, 0); + protected final static Version version = new Version(4, 3, 0, 1); protected final static Version majorVersion = new Version(version.getNumber(0)); protected final static Version databaseVersion = new Version(

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Build failed in Jenkins: isis-fish-nightly #1
by admin+ci-codelutin.com＠codelutin.com June 3, 2014

June 3, 2014

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Jenkins build is unstable: isis-fish-nightly » IsisFish #1
by admin+ci-codelutin.com＠codelutin.com June 3, 2014

June 3, 2014

See <http://ci.codelutin.com/jenkins/job/isis-fish-nightly/fr.ifremer$isis-fish/…>

1 17