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r4108 - in branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish: map simulator
by echatellier＠users.forge.codelutin.com 09 Sep '14

09 Sep '14

Author: echatellier Date: 2014-09-09 15:17:25 +0200 (Tue, 09 Sep 2014) New Revision: 4108 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4108 Log: fixes #5646: gestion des resultats n?\195?\169gatifs pour affichage sur la carte Modified: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/map/DefaultScale.java branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/map/Motif.java branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/map/Scale.java branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/simulator/SimulationParameter.java Modified: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/map/DefaultScale.java =================================================================== --- branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/map/DefaultScale.java 2014-09-09 10:06:34 UTC (rev 4107) +++ branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/map/DefaultScale.java 2014-09-09 13:17:25 UTC (rev 4108) @@ -92,15 +92,8 @@ } public int getValueAsRGB(double value) { + System.out.println(value); return (int) (value / (getMax() / 255.0)); } - public double getValueAsSqrtScale(double value) { - double scale = getValueAsScale(value); - if (scale < 0) { - return 0; - } - return Math.sqrt(scale); - } - } // DefaultScale Modified: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/map/Motif.java =================================================================== --- branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/map/Motif.java 2014-09-09 10:06:34 UTC (rev 4107) +++ branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/map/Motif.java 2014-09-09 13:17:25 UTC (rev 4108) @@ -197,8 +197,14 @@ Scale sc, DataMap datamap) { if (datamap.getValue() != 0) { int rgb = sc.getValueAsRGB(datamap.getValue()); + + // see http://forge.codelutin.com/issues/5646 + // cela peut se produire en cas de résultat incohérents + if (rgb < 0) { + rgb = 0; + } + Color lColor = new Color(255 - rgb, 255 - rgb, 255 - rgb, 255); - Color fColor = new Color(255 - rgb, 255 - rgb, 255 - rgb, 255); OMRect omrect; Modified: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/map/Scale.java =================================================================== --- branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/map/Scale.java 2014-09-09 10:06:34 UTC (rev 4107) +++ branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/map/Scale.java 2014-09-09 13:17:25 UTC (rev 4108) @@ -48,12 +48,4 @@ public int getValueAsRGB(double value); - /** - * Get the corresponding square root value between 0.0 and 1.0. - * - * @param value value to get sqrt scale - * @return sqrt scale - */ - public double getValueAsSqrtScale(double value); - } // Scale Modified: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/simulator/SimulationParameter.java =================================================================== --- branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/simulator/SimulationParameter.java 2014-09-09 10:06:34 UTC (rev 4107) +++ branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/simulator/SimulationParameter.java 2014-09-09 13:17:25 UTC (rev 4108) @@ -541,7 +541,7 @@ * * Default to "info". * - * @return simualtor log level + * @return simulator log level */ public String getSimulLogLevel();

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r4107 - in branches/4.3.0-log4j2: . src/main/java/fr/ifremer/isisfish/simulator/launcher src/main/java/fr/ifremer/isisfish/util src/test/java/fr/ifremer/isisfish/simulator src/test/java/fr/ifremer/isisfish/simulator/launcher src/test/java/fr/ifremer/isisfish/util
by echatellier＠users.forge.codelutin.com 09 Sep '14

09 Sep '14

Author: echatellier Date: 2014-09-09 12:06:34 +0200 (Tue, 09 Sep 2014) New Revision: 4107 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4107 Log: fixes #568: D?\195?\169pendances non incluses dans la simulation Modified: branches/4.3.0-log4j2/pom.xml branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationService.java branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/DependencyUtil.java branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/simulator/SimulationPreScriptTest.java branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/simulator/launcher/SimulationServiceTest.java branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/util/DependencyUtilTest.java Modified: branches/4.3.0-log4j2/pom.xml =================================================================== --- branches/4.3.0-log4j2/pom.xml 2014-09-01 11:05:03 UTC (rev 4106) +++ branches/4.3.0-log4j2/pom.xml 2014-09-09 10:06:34 UTC (rev 4107) @@ -216,10 +216,10 @@ </dependency> <dependency> - <groupId>org.slf4j</groupId> - <artifactId>slf4j-api</artifactId> - <version>1.7.7</version> - <scope>runtime</scope> + <groupId>org.slf4j</groupId> + <artifactId>slf4j-api</artifactId> + <version>1.7.7</version> + <scope>runtime</scope> </dependency> <dependency> @@ -323,6 +323,12 @@ <artifactId>ssj</artifactId> <version>2.5</version> <scope>runtime</scope> + <exclusions> + <exclusion> + <groupId>dsol</groupId> + <artifactId>dsol-xml</artifactId> + </exclusion> + </exclusions> </dependency>  @@ -342,10 +348,6 @@ <groupId>com.jcraft</groupId> </exclusion> <exclusion> - <artifactId>sqljet</artifactId> - <groupId>org.tmatesoft.sqljet</groupId> - </exclusion> - <exclusion> <artifactId>platform</artifactId> <groupId>net.java.dev.jna</groupId> </exclusion> Modified: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationService.java =================================================================== --- branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationService.java 2014-09-01 11:05:03 UTC (rev 4106) +++ branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationService.java 2014-09-09 10:06:34 UTC (rev 4107) @@ -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 @@ -47,8 +47,9 @@ import java.util.concurrent.Executors; import org.apache.commons.beanutils.BeanUtils; +import org.apache.commons.collections.CollectionUtils; import org.apache.commons.io.FileUtils; -import org.apache.commons.io.IOUtils; +import org.apache.commons.io.FilenameUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.mutable.MutableInt; import org.apache.commons.lang3.time.DurationFormatUtils; @@ -96,6 +97,7 @@ import fr.ifremer.isisfish.simulator.sensitivity.SensitivityUtils; import fr.ifremer.isisfish.simulator.sensitivity.domain.RuleDiscreteDomain; import fr.ifremer.isisfish.util.CompileHelper; +import fr.ifremer.isisfish.util.DependencyUtil; /** * Cette classe est responsable de conservation de toutes les simulations faites @@ -193,14 +195,6 @@ log.warn(t("Can't instantiate %s", value), eee); } } - - // fait un appel au moniteur - // pour reprendre le monitoring des simulation en cours - // TODO check this, don't restart monitoring on non ui launch - // moved to main() - //if (IsisFish.config.isLaunchUI()) { - // SimulationMonitor.getInstance().reloadConfig(this); - //} } /** @@ -403,7 +397,7 @@ } // on construit le zip de la simulation - File zip = prepareSimulationZipFile(control, localParameters, null, null, true); + File zip = prepareSimulationZipFile(control, localParameters, null, null); item.setSimulationZip(zip); if (localParameters.getUseSimulationPlan() && localParameters.isIndependentPlan()) { @@ -481,7 +475,7 @@ // on construit le zip de la simulation // in zip, there will be param "without" prescript - File zip = prepareSimulationZipFile(controlJustForZip, localParameters, xmlDesignPlan, sensitivityScenarios, true); + File zip = prepareSimulationZipFile(controlJustForZip, localParameters, xmlDesignPlan, sensitivityScenarios); // for each simulation, we neeed to launch a specific simulation // new simulation ids will be id + "_" + x @@ -715,48 +709,35 @@ * @param param les parametre de la simulation * @param xmlDesignPlan contenu xml des design plan * @param sensitivityScenarios used to add some extra files (such as rules) - * @param compile si vrai la version compile des fichiers Java est aussi - * mise dans le fichier zip. Cela peut servir pour les simulations locales - * pour ne pas recompiler pour chaque simulation avec plan de simulation * @return un zip de simulation pour une simulation pret a être faite * @throws SimulationException pour tout problème rencontré (IO,Topia...) */ protected File prepareSimulationZipFile(SimulationControl control, - SimulationParameter param, String xmlDesignPlan, SensitivityScenarios sensitivityScenarios, boolean compile) + SimulationParameter param, String xmlDesignPlan, SensitivityScenarios sensitivityScenarios) throws SimulationException { + try { - File tmpDirectory = FileUtil.createTempDirectory( - "isisfish-simulation-", "-preparation"); - //File regionXML = IsisConfig.getDataBackupFile(tmpDirectory); - File regionXML = new File(tmpDirectory, - SimulationStorage.DATA_BACKUP_FILENAME); + File tmpDirectory = FileUtil.createTempDirectory("isisfish-simulation-", "-preparation"); // sauvegarde des parametres Properties prop = param.toProperties(); - //File f = IsisConfig.getSimulationParametersFile(tmpDirectory); File f = new File(tmpDirectory, SimulationStorage.PARAMETERS_FILENAME); - FileOutputStream out = null; - try { - out = new FileOutputStream(f); + try (FileOutputStream out = new FileOutputStream(f)) { prop.store(out, "Parameters"); - } finally { - IOUtils.closeQuietly(out); } // backup pour toutes les simulations, pour eviter que l'utilisateur // ne puisse le modifier en meme temps control.setText(t("isisfish.message.backup.database.progress")); - RegionStorage region = RegionStorage.getRegion(param - .getRegionName()); + File regionBackup = new File(tmpDirectory, SimulationStorage.DATA_BACKUP_FILENAME); + RegionStorage region = RegionStorage.getRegion(param.getRegionName()); TopiaContext tc = region.getStorage().beginTransaction(); - tc.backup(regionXML, true); + tc.backup(regionBackup, true); tc.closeContext(); control.setText(t("isisfish.message.backup.database.finished")); - // copie de toutes regles a utiliser + // extract Rules defined in factors List<Rule> rules = param.getRules(); - - // FIXME small hack to add rules defined in simulations factors if (sensitivityScenarios != null) { for (Scenario sensitivityScenario : sensitivityScenarios.getScenarios()) { List<Factor> factors = sensitivityScenario.getFactors(); @@ -865,13 +846,6 @@ } } - // copie de tous les scripts a utiliser - // les script officiel prevalent sur les scripts communautés - FileUtil.copyRecursively(ScriptStorage.getCommunityScriptDirectory(), - tmpDirectory, ".*\\.java$"); - FileUtil.copyRecursively(ScriptStorage.getScriptDirectory(), - tmpDirectory, ".*\\.java$"); - // copie de tous les simulateurs a utiliser File simulatorFile = new File(SimulatorStorage.getSimulatorDirectory(), param.getSimulatorName()); if (!simulatorFile.isFile()) { @@ -881,14 +855,10 @@ SimulatorStorage.SIMULATOR_PATH + File.separator + param.getSimulatorName())); - // convert all file to UTF-8 - //convertAllFile(control, tmpDirectory); - - if (compile) { - compileAllFile(control, tmpDirectory); - } + // compile and add dependencies + compileAllFile(control, tmpDirectory); - // Sauvegarde du design plan en XML + // sauvegarde du design plan en XML if (!StringUtils.isEmpty(xmlDesignPlan)) { File simulationDesignPlanFile = SimulationStorage.getMexicoDesignPlan(tmpDirectory); FileUtils.writeStringToFile(simulationDesignPlanFile, xmlDesignPlan, "utf-8"); @@ -915,47 +885,6 @@ } - /* - * Convertit tous les fichiers du répertoire directory en UTF-8, - * pour eviter les erreurs d'encodage du la compilation - * sur un autre systeme ne supportant pas l'encodage courant. - * - * @param control le controleur - * @param directory le répertoire a convertir - * - protected void convertAllFile(SimulationControl control, File directory) { - - control.setText("Converting file to unicode"); - - List<File> fileToConvert = new ArrayList<File>(); - - List<File> tmp = FileUtil.find(new File(directory, - ExportStorage.EXPORT_PATH), ".*\\.java$", true); - fileToConvert.addAll(tmp); - - tmp = FileUtil.find(new File(directory, - SensitivityExportStorage.SENSITIVITY_EXPORT_PATH), ".*\\.java$", true); - fileToConvert.addAll(tmp); - - tmp = FileUtil.find(new File(directory, RuleStorage.RULE_PATH), - ".*\\.java$", true); - fileToConvert.addAll(tmp); - - tmp = FileUtil.find(new File(directory, - SimulationPlanStorage.SIMULATION_PLAN_PATH), ".*\\.java$", true); - fileToConvert.addAll(tmp); - - tmp = FileUtil.find( - new File(directory, SimulatorStorage.SIMULATOR_PATH), - ".*\\.java$", true); - fileToConvert.addAll(tmp); - - // - // Convertion - // - //CompileHelper.convertToUnicode(fileToConvert); - }*/ - /** * Compile les fichiers présent dans le répertoire passé en * parametre, ce répertoire est hiérarchisé en: rules, exports, simulators @@ -967,19 +896,21 @@ * * @param control le controleur * @param directory le répertoire où compiler + * @throws IOException */ - protected void compileAllFile(SimulationControl control, File directory) { + protected void compileAllFile(SimulationControl control, File directory) throws IOException { control.setText(t("isisfish.simulation.message.scriptscompilation")); long currentTime = System.nanoTime(); - // // Recherche des fichiers a compiler // On ne prend pas les scripts, car ils sont tous copiés mais pas // forcément util. Lors de la compilation des autres fichiers, les // script servant réellement seront automatiquement compilé - List<File> fileToCompile = new ArrayList<File>(); + List<File> fileToCompile = new ArrayList<>(); // *.java + List<File> fileToInpect = new ArrayList<>(); // *.class + Set<String> dependencies = new HashSet<String>(); // packages String[] modules = { ExportStorage.EXPORT_PATH, @@ -990,17 +921,46 @@ SimulationPlanStorage.SIMULATION_PLAN_PATH, SimulatorStorage.SIMULATOR_PATH }; - + for (String module : modules) { - List<File> tmp = FileUtil.find(new File(directory, module), ".*\\.java$", true); + File moduleDir = new File(directory, module); + List<File> tmp = FileUtil.find(moduleDir, ".*\\.java$", true); fileToCompile.addAll(tmp); + for (File srcFile : tmp) { + // source + fileToCompile.add(srcFile); + // class + File classFile = new File(srcFile.getAbsolutePath().replaceFirst("\\.java", ".class")); + fileToInpect.add(classFile); + // package + dependencies.add(module + "." + FilenameUtils.getBaseName(srcFile.getName())); + } } // // Compilation // - CompileHelper.compile(directory, fileToCompile, directory, null); + + // + // Check dependencies + // + Set<String> allDeps = DependencyUtil.extractDependencies(directory, fileToInpect); + Collection<String> missingDeps = CollectionUtils.subtract(allDeps, dependencies); + for (String missingDep : missingDeps) { + String relativePath = missingDep.replace('.', File.separatorChar) + ".java"; + // try official first + File srcFile = new File(IsisFish.config.getContextDatabaseDirectory(), relativePath); + if (!srcFile.isFile()) { + // if official file not exists, look for community file + srcFile = new File(IsisFish.config.getCommunityDatabaseDirectory(), missingDep.replace('.', File.separatorChar) + ".java"); + } + File destFile = new File(directory, missingDep.replace('.', File.separatorChar) + ".java"); + FileUtils.copyFile(srcFile, destFile); + } + // there is no need to compile this dependancies, they have been compiled by first compilation + // only add missing java files + long time = System.nanoTime() - currentTime; control.setText(t("isisfish.message.compilation.time", DurationFormatUtils.formatDuration(time / 1000000, "s'.'S"))); Modified: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/DependencyUtil.java =================================================================== --- branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/DependencyUtil.java 2014-09-01 11:05:03 UTC (rev 4106) +++ branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/DependencyUtil.java 2014-09-09 10:06:34 UTC (rev 4107) @@ -25,8 +25,13 @@ package fr.ifremer.isisfish.util; +import java.io.BufferedInputStream; +import java.io.File; +import java.io.FileInputStream; import java.io.IOException; import java.io.InputStream; +import java.util.ArrayList; +import java.util.Collection; import java.util.HashSet; import java.util.Set; import java.util.regex.Matcher; @@ -70,21 +75,56 @@ * Extrait les dépendences d'une class compilé à partir de son bytecode en ne conservant que * les dependances des scripts utilisateurs. * - * @param clazz la classe à analyser + * @param rootDirectory + * @param files ensemble de fichier à analyzer (fichiers .class) * @return extract class set */ - public static Set<String> extractDependencies(Class<?> clazz) { - return extractDependencies(clazz, true); + public static Set<String> extractDependencies(File rootDirectory, Collection<File> files) { + Set<String> deps = new HashSet<String>(); + Set<File> alreadyDone = new HashSet<File>(); + recursiveExtractDependencies(rootDirectory, files, alreadyDone, deps); + return deps; } + protected static void recursiveExtractDependencies(File rootDirectory, Collection<File> todoClassFiles, Set<File> alreadyDone, Set<String> deps) { + + // extract deps + for (File file : todoClassFiles) { + alreadyDone.add(file); + try (InputStream is = new BufferedInputStream(new FileInputStream(file))) { + Set<String> fileDeps = extractDependencies(is); + deps.addAll(fileDeps); + } catch (IOException ex) { + if (log.isErrorEnabled()) { + log.error("Can't extract dependencies", ex); + } + } + + } + + // convert deps to class filTopiaFlywayServicees + Collection<File> newClassFiles = new ArrayList<>(); + for (String dep : deps) { + String classRelative = dep.replace('.', File.separatorChar) + ".class"; + File classFile = new File(rootDirectory, classRelative); + if (!alreadyDone.contains(classFile)) { + newClassFiles.add(classFile); + } + } + + // make new recursion if necessary + if (!newClassFiles.isEmpty()) { + recursiveExtractDependencies(rootDirectory, newClassFiles, alreadyDone, deps); + } + } + /** * Extrait les dépendences d'une class compilé à partir de son bytecode. * * @param clazz la classe à analyser - * @param onlyUserScript only keep user script types * @return extract class set */ - public static Set<String> extractDependencies(Class<?> clazz, final boolean onlyUserScript) { + protected static Set<String> extractDependencies(InputStream clazzStream) { final Set<String> result = new HashSet<>(); // method body visitor @@ -92,59 +132,59 @@ @Override public AnnotationVisitor visitAnnotation(String desc, boolean visible) { - registerDescriptor(result, desc, onlyUserScript); + registerDescriptor(result, desc); return super.visitAnnotation(desc, visible); } @Override public AnnotationVisitor visitTypeAnnotation(int typeRef, TypePath typePath, String desc, boolean visible) { - registerDescriptor(result, desc, onlyUserScript); + registerDescriptor(result, desc); return super.visitTypeAnnotation(typeRef, typePath, desc, visible); } @Override public AnnotationVisitor visitParameterAnnotation(int parameter, String desc, boolean visible) { - registerDescriptor(result, desc, onlyUserScript); + registerDescriptor(result, desc); return super.visitParameterAnnotation(parameter, desc, visible); } @Override public void visitTypeInsn(int opcode, String type) { - registerType(result, type, onlyUserScript); + registerType(result, type); super.visitTypeInsn(opcode, type); } @Override public void visitFieldInsn(int opcode, String owner, String name, String desc) { - registerType(result, owner, onlyUserScript); - registerDescriptor(result, desc, onlyUserScript); + registerType(result, owner); + registerDescriptor(result, desc); super.visitFieldInsn(opcode, owner, name, desc); } @Override public void visitMethodInsn(int opcode, String owner, String name, String desc, boolean itf) { - registerType(result, owner, onlyUserScript); - registerDescriptor(result, desc, onlyUserScript); + registerType(result, owner); + registerDescriptor(result, desc); super.visitMethodInsn(opcode, owner, name, desc, itf); } @Override public void visitLdcInsn(Object cst) { if (cst instanceof Type) { - registerType(result, ((Type)cst).getClassName(), onlyUserScript); + registerType(result, ((Type)cst).getClassName()); } super.visitLdcInsn(cst); } @Override public void visitTryCatchBlock(Label start, Label end, Label handler, String type) { - registerType(result, type, onlyUserScript); + registerType(result, type); super.visitTryCatchBlock(start, end, handler, type); } @Override public void visitLocalVariable(String name, String desc, String signature, Label start, Label end, int index) { - registerDescriptor(result, desc, onlyUserScript); + registerDescriptor(result, desc); super.visitLocalVariable(name, desc, signature, start, end, index); } }; @@ -155,35 +195,35 @@ @Override public void visit(int version, int access, String name, String signature, String superName, String[] interfaces) { - registerType(result, superName, onlyUserScript); + registerType(result, superName); super.visit(version, access, name, signature, superName, interfaces); } @Override public AnnotationVisitor visitAnnotation(String desc, boolean visible) { - registerDescriptor(result, desc, onlyUserScript); + registerDescriptor(result, desc); return super.visitAnnotation(desc, visible); } @Override public FieldVisitor visitField(int access, String name, String desc, String signature, Object value) { - registerDescriptor(result, desc, onlyUserScript); + registerDescriptor(result, desc); return super.visitField(access, name, desc, signature, value); } @Override public MethodVisitor visitMethod(int access, String name, String desc, String signature, String[] exceptions) { - registerDescriptor(result, desc, onlyUserScript); + registerDescriptor(result, desc); return mv; } }; - // parse inpu class - try (InputStream in = clazz.getResourceAsStream("/" + clazz.getName().replace('.', '/') + ".class")) { - ClassReader classReader = new ClassReader(in); + // parse input class + try { + ClassReader classReader = new ClassReader(clazzStream); classReader.accept(visitor, 0); } catch (IOException ex) { if (log.isErrorEnabled()) { @@ -199,11 +239,10 @@ * * @param types types collection * @param type type to add - * @param onlyUserScript only keep user script types */ - protected static void registerType(Set<String> types, String type, boolean onlyUserScript) { + protected static void registerType(Set<String> types, String type) { //System.out.println("==> " + type); - if (!onlyUserScript || StringUtils.startsWithAny(type, + if (StringUtils.startsWithAny(type, ExportStorage.EXPORT_PATH, FormuleStorage.FORMULE_PATH, ObjectiveStorage.OBJECTIVE_PATH, @@ -227,25 +266,25 @@ * <li>Lfr/ifremer/isisfish/types/Month;</li> * <li>[Ljava/lang/String;</li> * <li>(Ljava/lang/Class;)Lorg/apache/commons/logging/Log;</li> + * </ul> * * @param types types collection * @param descriptor descriptor - * @param onlyUserScript only keep user script types */ - protected static void registerDescriptor(Set<String> types, String descriptor, boolean onlyUserScript) { + protected static void registerDescriptor(Set<String> types, String descriptor) { if (descriptor.startsWith("(")) { int endIndex = descriptor.indexOf(')'); - registerDescriptor(types, descriptor.substring(1, endIndex), onlyUserScript); - registerDescriptor(types, descriptor.substring(endIndex + 1), onlyUserScript); + registerDescriptor(types, descriptor.substring(1, endIndex)); + registerDescriptor(types, descriptor.substring(endIndex + 1)); } else { - Pattern pattern = Pattern.compile("\\[*L([^;]+);|\\[[ZBCSIFDJ]|[ZBCSIFDJ]"); + // full pattern : \\[*L([^;]+);|\\[[ZBCSIFDJ]|[ZBCSIFDJ] + // on exclut la fin (les types primitifs) pour ne conserver que la partie interessante + // du pattern qui nous concerne + Pattern pattern = Pattern.compile("\\[*L([^;]+);"); Matcher matcher = pattern.matcher(descriptor); while (matcher.find()) { String match = matcher.group(1); - // sinon c'est un type primitif - if (match != null) { - registerType(types, match, onlyUserScript); - } + registerType(types, match); } } } Modified: branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/simulator/SimulationPreScriptTest.java =================================================================== --- branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/simulator/SimulationPreScriptTest.java 2014-09-01 11:05:03 UTC (rev 4106) +++ branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/simulator/SimulationPreScriptTest.java 2014-09-09 10:06:34 UTC (rev 4107) @@ -31,9 +31,7 @@ import org.apache.commons.beanutils.BeanUtils; import org.apache.commons.beanutils.ConvertUtilsBean; -import org.junit.After; import org.junit.Assert; -import org.junit.Before; import org.junit.Test; import org.nuiton.math.matrix.MatrixFactory; import org.nuiton.math.matrix.MatrixND; @@ -55,21 +53,6 @@ */ public class SimulationPreScriptTest extends AbstractIsisFishTest { - @Before - public void setUp() throws Exception { - // not do it in @BeforeClass - // test will fail ! - init(); - // very important , other test wil fail with that - //System.setProperty("hibernate.hbm2ddl.auto", "create"); - } - - @After - public void tearDown() { - // very important , other test wil fail with that - //System.clearProperty("hibernate.hbm2ddl.auto"); - } - /** * Test que les chaine represantant des matrices sont correctement * transformée en MatrixND. Modified: branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/simulator/launcher/SimulationServiceTest.java =================================================================== --- branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/simulator/launcher/SimulationServiceTest.java 2014-09-01 11:05:03 UTC (rev 4106) +++ branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/simulator/launcher/SimulationServiceTest.java 2014-09-09 10:06:34 UTC (rev 4107) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2006 - 2011 Ifremer, Code Lutin, Chatellier Eric + * Copyright (C) 2006 - 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 @@ -25,6 +25,7 @@ package fr.ifremer.isisfish.simulator.launcher; +import java.io.File; import java.util.ArrayList; import java.util.List; import java.util.Properties; @@ -34,7 +35,6 @@ import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.junit.Assert; -import org.junit.Before; import org.junit.Ignore; import org.junit.Test; import org.nuiton.math.matrix.MatrixFactory; @@ -47,6 +47,9 @@ import fr.ifremer.isisfish.IsisFishException; import fr.ifremer.isisfish.datastore.RegionStorage; import fr.ifremer.isisfish.datastore.RuleStorage; +import fr.ifremer.isisfish.datastore.ScriptStorage; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.datastore.SimulatorStorage; import fr.ifremer.isisfish.datastore.StorageException; import fr.ifremer.isisfish.entities.Population; import fr.ifremer.isisfish.entities.PopulationGroup; @@ -84,11 +87,61 @@ /** Commons logging log. */ private static Log log = LogFactory.getLog(SimulationServiceTest.class); - @Before - public void setUp() throws Exception { - // not do it in @BeforeClass - // test will fail ! - AbstractIsisFishTest.init(); + /** + * Lance une simulation simple avec le simulateur par cellule. + * + * Test is wrong if it take more than 2 min. + * + * @throws InterruptedException + */ + @Test(timeout=120 * 1000) + public void testSimulationEffortByCell() throws InterruptedException { + + SimulationParameter params = new SimulationParameterImpl(); + // set params region + params.setRegionName("DemoRegion"); + // simulator + params.setSimulatorName("SimulatorEffortByCell.java"); + // set population + List<Population> pops = new ArrayList<Population>(); + Population pop = new PopulationImpl(); + pop.setName("test population"); + pop.setPopulationGroup(new ArrayList<PopulationGroup>()); + pop.setPopulationZone(new ArrayList<Zone>()); + pops.add(pop); + params.setPopulations(pops); + // strat + List<Strategy> strats = new ArrayList<Strategy>(); + Strategy strategy = new StrategyImpl(); + strategy.setName("stratest"); + strats.add(strategy); + params.setStrategies(strats); + // number of year + params.setNumberOfYear(1); + + // run simulation + SimulationService service = SimulationService.getService(); + SimulatorLauncher launcher = new InProcessSimulatorLauncher(); + service.addSimulationLauncher(launcher); + String simulationId = "effort by cell test number 1"; + service.submit("effort by cell test number 1", params, launcher, 0); + + // temporise la fin de test , sinon junit tue tous les process + do { + Thread.sleep(2000); + } while (!service.jobs.isEmpty()); + + // suite au changement de la compilation, on vérifie que certains fichier java + // doivent être automatiquement inclut dans les sources + File simDir = SimulationStorage.getSimulationDirectory(simulationId); + File simulatorDir = new File(simDir, SimulatorStorage.SIMULATOR_PATH); + File scriptDir = new File(simDir, ScriptStorage.SCRIPT_PATH); + Assert.assertTrue(new File(simulatorDir, "DefaultSimulator.java").exists()); + Assert.assertTrue(new File(simulatorDir, "SimulatorEffortByCell.java").exists()); + Assert.assertTrue(new File(scriptDir, "ResultName.java").exists()); + Assert.assertTrue(new File(scriptDir, "SiMatrix.java").exists()); + Assert.assertTrue(new File(scriptDir, "GravityModel.java").exists()); + Assert.assertTrue(new File(scriptDir, "RuleUtil.java").exists()); } /** @@ -180,9 +233,11 @@ * Lance une simulation avec des facteurs de sensibilité. * * Test is wrong if it take more than 2 min. + * + * @throws InterruptedException */ @Test(timeout=120 * 1000) - public void testRunSensivitySimulation() { + public void testRunSensivitySimulation() throws InterruptedException { SimulationParameter params = new SimulationParameterImpl(); // set params region @@ -216,15 +271,10 @@ sensitivityAnalysis, designPlan); // temporise la fin de test , sinon junit tue tous les process - try { - do { - Thread.sleep(2000); - } while (!service.jobs.isEmpty()); - } catch (InterruptedException e) { - if (log.isErrorEnabled()) { - log.error("Can't wait wimulation to end", e); - } - } + do { + Thread.sleep(2000); + } while (!service.jobs.isEmpty()); + } /** Modified: branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/util/DependencyUtilTest.java =================================================================== --- branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/util/DependencyUtilTest.java 2014-09-01 11:05:03 UTC (rev 4106) +++ branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/util/DependencyUtilTest.java 2014-09-09 10:06:34 UTC (rev 4107) @@ -24,13 +24,18 @@ */ package fr.ifremer.isisfish.util; +import java.io.File; +import java.io.IOException; +import java.util.Collections; import java.util.Set; import org.junit.Assert; import org.junit.Test; import fr.ifremer.isisfish.AbstractIsisFishTest; +import fr.ifremer.isisfish.IsisFish; import fr.ifremer.isisfish.IsisFishException; +import fr.ifremer.isisfish.datastore.JavaSourceStorage; import fr.ifremer.isisfish.datastore.RuleStorage; import fr.ifremer.isisfish.datastore.ScriptStorage; import fr.ifremer.isisfish.datastore.SimulatorStorage; @@ -43,18 +48,39 @@ public class DependencyUtilTest extends AbstractIsisFishTest { /** + * Extract dependency for test. + * + * @param storage storage + * @return deps + * @throws IsisFishException + */ + protected static Set<String> extractDependencies(JavaSourceStorage storage) throws IsisFishException { + String clazzName = storage.getCodeClass().getName(); + File classFile = new File(IsisFish.config.getCompileDirectory(), clazzName.replace('.', File.separatorChar) + ".class"); + Set<String> result = DependencyUtil.extractDependencies(IsisFish.config.getCompileDirectory(), Collections.singletonList(classFile)); + return result; + } + + /** * Récupère une classe parmis les scripts de test et vérifie que les dépendances sont bien * extraites. * * @throws IsisFishException + * @throws IOException */ @Test - public void testExtractDependencies1() throws IsisFishException { - SimulatorStorage simulatorByCell = SimulatorStorage.getSimulator("SimulatorEffortByCell"); - Class<?> clazz = simulatorByCell.getCodeClass(); - Set<String> deps = DependencyUtil.extractDependencies(clazz, false); - Assert.assertTrue(deps.size() >= 10); + public void testExtractDependencies1() throws IsisFishException, IOException { + SimulatorStorage script = SimulatorStorage.getSimulator("SimulatorEffortByCell"); + Set<String> deps = extractDependencies(script); + // premier niveau Assert.assertTrue(deps.contains("simulators.DefaultSimulator")); + // deuxieme niveau de dependance + Assert.assertTrue(deps.contains("scripts.SiMatrix")); + Assert.assertTrue(deps.contains("scripts.GravityModel")); + // troisieme niveau + Assert.assertTrue(deps.contains("scripts.MinimisationUtil")); + Assert.assertTrue(deps.contains("scripts.ObjectiveFunction")); + Assert.assertTrue(deps.contains("scripts.ObjectiveFunctionBaranov")); } /** @@ -62,13 +88,12 @@ * extraites. * * @throws IsisFishException + * @throws IOException */ @Test - public void testExtractDependencies2() throws IsisFishException { - SimulatorStorage simulator = SimulatorStorage.getSimulator("DefaultSimulator"); - Class<?> clazz = simulator.getCodeClass(); - Set<String> deps = DependencyUtil.extractDependencies(clazz, false); - Assert.assertTrue(deps.size() >= 35); + public void testExtractDependencies2() throws IsisFishException, IOException { + SimulatorStorage script = SimulatorStorage.getSimulator("DefaultSimulator"); + Set<String> deps = extractDependencies(script); Assert.assertTrue(deps.contains("scripts.GravityModel")); Assert.assertTrue(deps.contains("scripts.ResultName")); Assert.assertTrue(deps.contains("scripts.SiMatrix")); @@ -80,13 +105,12 @@ * extraites. * * @throws IsisFishException + * @throws IOException */ @Test - public void testExtractDependencies3() throws IsisFishException { - RuleStorage cantonnement = RuleStorage.getRule("Cantonnement"); - Class<?> clazz = cantonnement.getCodeClass(); - Set<String> deps = DependencyUtil.extractDependencies(clazz, false); - Assert.assertTrue(deps.size() >= 30); + public void testExtractDependencies3() throws IsisFishException, IOException { + RuleStorage script = RuleStorage.getRule("Cantonnement"); + Set<String> deps = extractDependencies(script); Assert.assertTrue(deps.contains("scripts.ResultName")); } @@ -95,13 +119,12 @@ * extraites. * * @throws IsisFishException + * @throws IOException */ @Test - public void testExtractDependencies4() throws IsisFishException { + public void testExtractDependencies4() throws IsisFishException, IOException { ScriptStorage script = ScriptStorage.getScript("SiMatrix"); - Class<?> clazz = script.getCodeClass(); - Set<String> deps = DependencyUtil.extractDependencies(clazz, false); - Assert.assertTrue(deps.size() >= 51); + Set<String> deps = extractDependencies(script); Assert.assertTrue(deps.contains("scripts.ObjectiveFunctionBaranov")); Assert.assertTrue(deps.contains("scripts.ObjectiveFunction")); Assert.assertTrue(deps.contains("scripts.MinimisationUtil")); @@ -113,13 +136,12 @@ * extraites. * * @throws IsisFishException + * @throws IOException */ @Test - public void testExtractDependencies5() throws IsisFishException { + public void testExtractDependencies5() throws IsisFishException, IOException { ScriptStorage script = ScriptStorage.getScript("GravityModel"); - Class<?> clazz = script.getCodeClass(); - Set<String> deps = DependencyUtil.extractDependencies(clazz, false); - Assert.assertTrue(deps.size() >= 31); + Set<String> deps = extractDependencies(script); Assert.assertTrue(deps.contains("scripts.SiMatrix")); Assert.assertTrue(deps.contains("scripts.ResultName")); } @@ -129,14 +151,12 @@ * extraites. * * @throws IsisFishException + * @throws IOException */ @Test - public void testExtractDependencies6() throws IsisFishException { + public void testExtractDependencies6() throws IsisFishException, IOException { ScriptStorage script = ScriptStorage.getScript("ObjectiveFunctionBaranov"); - Class<?> clazz = script.getCodeClass(); - Set<String> deps = DependencyUtil.extractDependencies(clazz, false); - Assert.assertTrue(deps.size() >= 4); + Set<String> deps = extractDependencies(script); Assert.assertTrue(deps.contains("scripts.ObjectiveFunction")); - Assert.assertTrue(deps.contains("fr.ifremer.isisfish.util.Nocache")); } }

1 0

r4106 - branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/ssh
by echatellier＠users.forge.codelutin.com 01 Sep '14

01 Sep '14

Author: echatellier Date: 2014-09-01 13:05:03 +0200 (Mon, 01 Sep 2014) New Revision: 4106 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4106 Log: Simplify code Modified: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/ssh/ProxyCommand.java Modified: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/ssh/ProxyCommand.java =================================================================== --- branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/ssh/ProxyCommand.java 2014-09-01 11:04:37 UTC (rev 4105) +++ branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/ssh/ProxyCommand.java 2014-09-01 11:05:03 UTC (rev 4106) @@ -51,7 +51,7 @@ 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()); + fullCommand = fullCommand.replace("%p", String.valueOf(port)); p = Runtime.getRuntime().exec(fullCommand); in = p.getInputStream(); out = p.getOutputStream();

1 0

r4105 - branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/simulator/sensitivity
by echatellier＠users.forge.codelutin.com 01 Sep '14

01 Sep '14

Author: echatellier Date: 2014-09-01 13:04:37 +0200 (Mon, 01 Sep 2014) New Revision: 4105 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4105 Log: Fix invalid cast Modified: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityAnalysis.java Modified: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityAnalysis.java =================================================================== --- branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityAnalysis.java 2014-08-29 13:39:04 UTC (rev 4104) +++ branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityAnalysis.java 2014-09-01 11:04:37 UTC (rev 4105) @@ -416,7 +416,7 @@ Distribution distribution = domain.getDistribution(); double result = 0; if (distribution == Distribution.QUNIFPC) { - Object reference = (Double)domain.getDistributionParameter(Distribution.QUNIFPC.getDistibutionParams()[0].getName()); + Object reference = domain.getDistributionParameter(Distribution.QUNIFPC.getDistibutionParams()[0].getName()); if (reference instanceof MatrixND) { result = min ? 0 : 1; } else {

1 0

r4104 - in branches/4.3.0-log4j2: . src/main/java/fr/ifremer/isisfish/util src/test/java/fr/ifremer/isisfish/util
by echatellier＠users.forge.codelutin.com 29 Aug '14

29 Aug '14

Author: echatellier Date: 2014-08-29 15:39:04 +0200 (Fri, 29 Aug 2014) New Revision: 4104 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4104 Log: refs #568: D?\195?\169pendances non incluses dans la simulation Added: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/DependencyUtil.java branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/util/DependencyUtilTest.java Modified: branches/4.3.0-log4j2/pom.xml Modified: branches/4.3.0-log4j2/pom.xml =================================================================== --- branches/4.3.0-log4j2/pom.xml 2014-08-29 08:58:39 UTC (rev 4103) +++ branches/4.3.0-log4j2/pom.xml 2014-08-29 13:39:04 UTC (rev 4104) @@ -75,6 +75,13 @@ </dependency> <dependency> + <groupId>org.ow2.asm</groupId> + <artifactId>asm</artifactId> + <version>5.0.3</version> + <scope>compile</scope> + </dependency> + + <dependency> <groupId>org.nuiton</groupId> <artifactId>nuiton-profiling</artifactId> <version>3.0</version> @@ -325,6 +332,24 @@ <artifactId>svnkit</artifactId> <version>1.8.5</version> <scope>compile</scope> + <exclusions> + <exclusion> + <artifactId>jna</artifactId> + <groupId>net.java.dev.jna</groupId> + </exclusion> + <exclusion> + <artifactId>jsch.agentproxy.connector-factory</artifactId> + <groupId>com.jcraft</groupId> + </exclusion> + <exclusion> + <artifactId>sqljet</artifactId> + <groupId>org.tmatesoft.sqljet</groupId> + </exclusion> + <exclusion> + <artifactId>platform</artifactId> + <groupId>net.java.dev.jna</groupId> + </exclusion> + </exclusions> </dependency>  @@ -352,13 +377,6 @@ <groupId>junit</groupId> <artifactId>junit</artifactId> </dependency> - - <dependency> - <groupId>org.hamcrest</groupId> - <artifactId>hamcrest-core</artifactId> - <version>1.3</version> - <scope>test</scope> - </dependency> </dependencies>  Added: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/DependencyUtil.java =================================================================== --- branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/DependencyUtil.java (rev 0) +++ branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/DependencyUtil.java 2014-08-29 13:39:04 UTC (rev 4104) @@ -0,0 +1,252 @@ +/* + * #%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; + +import java.io.IOException; +import java.io.InputStream; +import java.util.HashSet; +import java.util.Set; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.objectweb.asm.AnnotationVisitor; +import org.objectweb.asm.ClassReader; +import org.objectweb.asm.ClassVisitor; +import org.objectweb.asm.FieldVisitor; +import org.objectweb.asm.Label; +import org.objectweb.asm.MethodVisitor; +import org.objectweb.asm.Opcodes; +import org.objectweb.asm.Type; +import org.objectweb.asm.TypePath; + +import fr.ifremer.isisfish.datastore.ExportStorage; +import fr.ifremer.isisfish.datastore.FormuleStorage; +import fr.ifremer.isisfish.datastore.ObjectiveStorage; +import fr.ifremer.isisfish.datastore.OptimizationStorage; +import fr.ifremer.isisfish.datastore.RuleStorage; +import fr.ifremer.isisfish.datastore.ScriptStorage; +import fr.ifremer.isisfish.datastore.SensitivityAnalysisStorage; +import fr.ifremer.isisfish.datastore.SensitivityExportStorage; +import fr.ifremer.isisfish.datastore.SimulationPlanStorage; +import fr.ifremer.isisfish.datastore.SimulatorStorage; + +/** + * Class utilitaire chargées d'inspecter le bytecode de certaines classe des scripts utilisateur + * d'IsisFish pour en extraire des informations. + * + * @author Eric Chatellier + */ +public class DependencyUtil { + + private static final Log log = LogFactory.getLog(DependencyUtil.class); + + /** + * Extrait les dépendences d'une class compilé à partir de son bytecode en ne conservant que + * les dependances des scripts utilisateurs. + * + * @param clazz la classe à analyser + * @return extract class set + */ + public static Set<String> extractDependencies(Class<?> clazz) { + return extractDependencies(clazz, true); + } + + /** + * Extrait les dépendences d'une class compilé à partir de son bytecode. + * + * @param clazz la classe à analyser + * @param onlyUserScript only keep user script types + * @return extract class set + */ + public static Set<String> extractDependencies(Class<?> clazz, final boolean onlyUserScript) { + final Set<String> result = new HashSet<>(); + + // method body visitor + final MethodVisitor mv = new MethodVisitor(Opcodes.ASM5) { + + @Override + public AnnotationVisitor visitAnnotation(String desc, boolean visible) { + registerDescriptor(result, desc, onlyUserScript); + return super.visitAnnotation(desc, visible); + } + + @Override + public AnnotationVisitor visitTypeAnnotation(int typeRef, TypePath typePath, String desc, boolean visible) { + registerDescriptor(result, desc, onlyUserScript); + return super.visitTypeAnnotation(typeRef, typePath, desc, visible); + } + + @Override + public AnnotationVisitor visitParameterAnnotation(int parameter, String desc, boolean visible) { + registerDescriptor(result, desc, onlyUserScript); + return super.visitParameterAnnotation(parameter, desc, visible); + } + + @Override + public void visitTypeInsn(int opcode, String type) { + registerType(result, type, onlyUserScript); + super.visitTypeInsn(opcode, type); + } + + @Override + public void visitFieldInsn(int opcode, String owner, String name, String desc) { + registerType(result, owner, onlyUserScript); + registerDescriptor(result, desc, onlyUserScript); + super.visitFieldInsn(opcode, owner, name, desc); + } + + @Override + public void visitMethodInsn(int opcode, String owner, String name, String desc, boolean itf) { + registerType(result, owner, onlyUserScript); + registerDescriptor(result, desc, onlyUserScript); + super.visitMethodInsn(opcode, owner, name, desc, itf); + } + + @Override + public void visitLdcInsn(Object cst) { + if (cst instanceof Type) { + registerType(result, ((Type)cst).getClassName(), onlyUserScript); + } + super.visitLdcInsn(cst); + } + + @Override + public void visitTryCatchBlock(Label start, Label end, Label handler, String type) { + registerType(result, type, onlyUserScript); + super.visitTryCatchBlock(start, end, handler, type); + } + + @Override + public void visitLocalVariable(String name, String desc, String signature, Label start, Label end, int index) { + registerDescriptor(result, desc, onlyUserScript); + super.visitLocalVariable(name, desc, signature, start, end, index); + } + }; + + // class visitor + ClassVisitor visitor = new ClassVisitor(Opcodes.ASM5) { + + @Override + public void visit(int version, int access, String name, + String signature, String superName, String[] interfaces) { + registerType(result, superName, onlyUserScript); + super.visit(version, access, name, signature, superName, interfaces); + } + + @Override + public AnnotationVisitor visitAnnotation(String desc, + boolean visible) { + registerDescriptor(result, desc, onlyUserScript); + return super.visitAnnotation(desc, visible); + } + + @Override + public FieldVisitor visitField(int access, String name, + String desc, String signature, Object value) { + registerDescriptor(result, desc, onlyUserScript); + return super.visitField(access, name, desc, signature, value); + } + + @Override + public MethodVisitor visitMethod(int access, String name, + String desc, String signature, String[] exceptions) { + registerDescriptor(result, desc, onlyUserScript); + return mv; + } + }; + + // parse inpu class + try (InputStream in = clazz.getResourceAsStream("/" + clazz.getName().replace('.', '/') + ".class")) { + ClassReader classReader = new ClassReader(in); + classReader.accept(visitor, 0); + } catch (IOException ex) { + if (log.isErrorEnabled()) { + log.error("Can't extract dependencies", ex); + } + } + + return result; + } + + /** + * Register type if necessary (depends on another user script). + * + * @param types types collection + * @param type type to add + * @param onlyUserScript only keep user script types + */ + protected static void registerType(Set<String> types, String type, boolean onlyUserScript) { + //System.out.println("==> " + type); + if (!onlyUserScript || StringUtils.startsWithAny(type, + ExportStorage.EXPORT_PATH, + FormuleStorage.FORMULE_PATH, + ObjectiveStorage.OBJECTIVE_PATH, + OptimizationStorage.OPTIMIZATION_PATH, + RuleStorage.RULE_PATH, + ScriptStorage.SCRIPT_PATH, + SensitivityAnalysisStorage.SENSITIVITY_ANALYSIS_PATH, + SensitivityExportStorage.SENSITIVITY_EXPORT_PATH, + SimulationPlanStorage.SIMULATION_PLAN_PATH, + SimulatorStorage.SIMULATOR_PATH)) { + String dotType = type.replace('/', '.'); + types.add(dotType); + } + } + + /** + * Clean type to extract valid class name. + * + * Ex: + * <ul> + * <li>Lfr/ifremer/isisfish/types/Month;</li> + * <li>[Ljava/lang/String;</li> + * <li>(Ljava/lang/Class;)Lorg/apache/commons/logging/Log;</li> + * + * @param types types collection + * @param descriptor descriptor + * @param onlyUserScript only keep user script types + */ + protected static void registerDescriptor(Set<String> types, String descriptor, boolean onlyUserScript) { + if (descriptor.startsWith("(")) { + int endIndex = descriptor.indexOf(')'); + registerDescriptor(types, descriptor.substring(1, endIndex), onlyUserScript); + registerDescriptor(types, descriptor.substring(endIndex + 1), onlyUserScript); + } else { + Pattern pattern = Pattern.compile("\\[*L([^;]+);|\\[[ZBCSIFDJ]|[ZBCSIFDJ]"); + Matcher matcher = pattern.matcher(descriptor); + while (matcher.find()) { + String match = matcher.group(1); + // sinon c'est un type primitif + if (match != null) { + registerType(types, match, onlyUserScript); + } + } + } + } +} Property changes on: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/DependencyUtil.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native Added: branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/util/DependencyUtilTest.java =================================================================== --- branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/util/DependencyUtilTest.java (rev 0) +++ branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/util/DependencyUtilTest.java 2014-08-29 13:39:04 UTC (rev 4104) @@ -0,0 +1,142 @@ +/* + * #%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; + +import java.util.Set; + +import org.junit.Assert; +import org.junit.Test; + +import fr.ifremer.isisfish.AbstractIsisFishTest; +import fr.ifremer.isisfish.IsisFishException; +import fr.ifremer.isisfish.datastore.RuleStorage; +import fr.ifremer.isisfish.datastore.ScriptStorage; +import fr.ifremer.isisfish.datastore.SimulatorStorage; + +/** + * Test concernant la gestion du bytecode des scripts utilisateur. + * + * @author Eric Chatellier + */ +public class DependencyUtilTest extends AbstractIsisFishTest { + + /** + * Récupère une classe parmis les scripts de test et vérifie que les dépendances sont bien + * extraites. + * + * @throws IsisFishException + */ + @Test + public void testExtractDependencies1() throws IsisFishException { + SimulatorStorage simulatorByCell = SimulatorStorage.getSimulator("SimulatorEffortByCell"); + Class<?> clazz = simulatorByCell.getCodeClass(); + Set<String> deps = DependencyUtil.extractDependencies(clazz, false); + Assert.assertTrue(deps.size() >= 10); + Assert.assertTrue(deps.contains("simulators.DefaultSimulator")); + } + + /** + * Récupère une classe parmis les scripts de test et vérifie que les dépendances sont bien + * extraites. + * + * @throws IsisFishException + */ + @Test + public void testExtractDependencies2() throws IsisFishException { + SimulatorStorage simulator = SimulatorStorage.getSimulator("DefaultSimulator"); + Class<?> clazz = simulator.getCodeClass(); + Set<String> deps = DependencyUtil.extractDependencies(clazz, false); + Assert.assertTrue(deps.size() >= 35); + Assert.assertTrue(deps.contains("scripts.GravityModel")); + Assert.assertTrue(deps.contains("scripts.ResultName")); + Assert.assertTrue(deps.contains("scripts.SiMatrix")); + + } + + /** + * Récupère une classe parmis les scripts de test et vérifie que les dépendances sont bien + * extraites. + * + * @throws IsisFishException + */ + @Test + public void testExtractDependencies3() throws IsisFishException { + RuleStorage cantonnement = RuleStorage.getRule("Cantonnement"); + Class<?> clazz = cantonnement.getCodeClass(); + Set<String> deps = DependencyUtil.extractDependencies(clazz, false); + Assert.assertTrue(deps.size() >= 30); + Assert.assertTrue(deps.contains("scripts.ResultName")); + } + + /** + * Récupère une classe parmis les scripts de test et vérifie que les dépendances sont bien + * extraites. + * + * @throws IsisFishException + */ + @Test + public void testExtractDependencies4() throws IsisFishException { + ScriptStorage script = ScriptStorage.getScript("SiMatrix"); + Class<?> clazz = script.getCodeClass(); + Set<String> deps = DependencyUtil.extractDependencies(clazz, false); + Assert.assertTrue(deps.size() >= 51); + Assert.assertTrue(deps.contains("scripts.ObjectiveFunctionBaranov")); + Assert.assertTrue(deps.contains("scripts.ObjectiveFunction")); + Assert.assertTrue(deps.contains("scripts.MinimisationUtil")); + Assert.assertTrue(deps.contains("scripts.ResultName")); + } + + /** + * Récupère une classe parmis les scripts de test et vérifie que les dépendances sont bien + * extraites. + * + * @throws IsisFishException + */ + @Test + public void testExtractDependencies5() throws IsisFishException { + ScriptStorage script = ScriptStorage.getScript("GravityModel"); + Class<?> clazz = script.getCodeClass(); + Set<String> deps = DependencyUtil.extractDependencies(clazz, false); + Assert.assertTrue(deps.size() >= 31); + Assert.assertTrue(deps.contains("scripts.SiMatrix")); + Assert.assertTrue(deps.contains("scripts.ResultName")); + } + + /** + * Récupère une classe parmis les scripts de test et vérifie que les dépendances sont bien + * extraites. + * + * @throws IsisFishException + */ + @Test + public void testExtractDependencies6() throws IsisFishException { + ScriptStorage script = ScriptStorage.getScript("ObjectiveFunctionBaranov"); + Class<?> clazz = script.getCodeClass(); + Set<String> deps = DependencyUtil.extractDependencies(clazz, false); + Assert.assertTrue(deps.size() >= 4); + Assert.assertTrue(deps.contains("scripts.ObjectiveFunction")); + Assert.assertTrue(deps.contains("fr.ifremer.isisfish.util.Nocache")); + } +} Property changes on: branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/util/DependencyUtilTest.java ___________________________________________________________________ Added: svn:eol-style + native Added: svn:keywords + Author Date Id Revision HeadURL

1 0

r4103 - branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/entity
by echatellier＠users.forge.codelutin.com 29 Aug '14

29 Aug '14

Author: echatellier Date: 2014-08-29 10:58:39 +0200 (Fri, 29 Aug 2014) New Revision: 4103 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4103 Log: Remove useless hamcrest complicated code Modified: branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/entity/TopiaDAOTest.java Modified: branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/entity/TopiaDAOTest.java =================================================================== --- branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/entity/TopiaDAOTest.java 2014-08-28 15:52:19 UTC (rev 4102) +++ branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/entity/TopiaDAOTest.java 2014-08-29 08:58:39 UTC (rev 4103) @@ -3,7 +3,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2010 - 2012 Ifremer, Codelutin, Chatellier Eric + * Copyright (C) 2010 - 2014 Ifremer, Codelutin, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -26,7 +26,6 @@ import java.io.IOException; import java.util.List; -import org.hamcrest.CoreMatchers; import org.junit.Assert; import org.junit.Test; import org.nuiton.topia.TopiaContext; @@ -84,7 +83,7 @@ population2.setName("thon"); allPopulation = populationDAO.findAll(); Assert.assertEquals(2, allPopulation.size()); - Assert.assertThat(allPopulation, CoreMatchers.hasItem(population2)); + Assert.assertTrue(allPopulation.contains(population2)); context.rollbackTransaction(); @@ -93,7 +92,7 @@ population3.setName("requin"); allPopulation = populationDAO.findAll(); Assert.assertEquals(2, allPopulation.size()); - Assert.assertThat(allPopulation, CoreMatchers.hasItem(population3)); + Assert.assertTrue(allPopulation.contains(population3)); context.commitTransaction(); simulation.closeStorage();

1 0

r4102 - in branches/4.3.0-log4j2: . src/main/assembly
by echatellier＠users.forge.codelutin.com 28 Aug '14

28 Aug '14

Author: echatellier Date: 2014-08-28 17:52:19 +0200 (Thu, 28 Aug 2014) New Revision: 4102 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4102 Log: Fix assembly and default memory Added: branches/4.3.0-log4j2/src/main/assembly/isisfish-log4j2.xml Removed: branches/4.3.0-log4j2/src/main/assembly/isisfish-log4j.properties Modified: branches/4.3.0-log4j2/pom.xml branches/4.3.0-log4j2/src/main/assembly/bin.xml branches/4.3.0-log4j2/src/main/assembly/isisfish.bat branches/4.3.0-log4j2/src/main/assembly/isisfish.sh Modified: branches/4.3.0-log4j2/pom.xml =================================================================== --- branches/4.3.0-log4j2/pom.xml 2014-08-28 14:25:25 UTC (rev 4101) +++ branches/4.3.0-log4j2/pom.xml 2014-08-28 15:52:19 UTC (rev 4102) @@ -364,7 +364,7 @@    - <name>IsisFish</name> + <name>ISIS-Fish</name> <description>Simulateur de pecherie complexe.</description> <inceptionYear>1999</inceptionYear> Modified: branches/4.3.0-log4j2/src/main/assembly/bin.xml =================================================================== --- branches/4.3.0-log4j2/src/main/assembly/bin.xml 2014-08-28 14:25:25 UTC (rev 4101) +++ branches/4.3.0-log4j2/src/main/assembly/bin.xml 2014-08-28 15:52:19 UTC (rev 4102) @@ -6,7 +6,7 @@ $Id$ $HeadURL$ %% - Copyright (C) 1999 - 2013 Ifremer, CodeLutin, Eric Chatellier + Copyright (C) 1999 - 2014 Ifremer, CodeLutin, Eric Chatellier %% This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as @@ -60,7 +60,7 @@ <directory>src/main/assembly</directory> <outputDirectory /> <includes> - <include>isisfish-log4j.properties</include> + <include>isisfish-log4j.xml</include> </includes> </fileSet> </fileSets> Deleted: branches/4.3.0-log4j2/src/main/assembly/isisfish-log4j.properties =================================================================== --- branches/4.3.0-log4j2/src/main/assembly/isisfish-log4j.properties 2014-08-28 14:25:25 UTC (rev 4101) +++ branches/4.3.0-log4j2/src/main/assembly/isisfish-log4j.properties 2014-08-28 15:52:19 UTC (rev 4102) @@ -1,45 +0,0 @@ -### -# #%L -# IsisFish -# -# $Id$ -# $HeadURL$ -# %% -# Copyright (C) 2011 - 2013 Ifremer, CodeLutin, Chatellier Eric -# %% -# This program is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as -# 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% -### -# Global logging configuration -log4j.rootLogger=ERROR, stdout - -# Console output... -log4j.appender.stdout=org.apache.log4j.ConsoleAppender -log4j.appender.stdout.layout=org.apache.log4j.PatternLayout -log4j.appender.stdout.layout.ConversionPattern=%5p [%t] (%F:%L) %M - %m%n - -# Package level -log4j.logger.fr.ifremer.isisfish=INFO -log4j.logger.analyseplans=INFO -log4j.logger.exports=INFO -log4j.logger.formules=INFO -log4j.logger.rules=INFO -log4j.logger.scripts=INFO -log4j.logger.sensitivity=INFO -log4j.logger.sensitivityexports=INFO -log4j.logger.simulators=INFO - -# Add your configuration here -#log4j.logger.org.nuiton.j2r=DEBUG Added: branches/4.3.0-log4j2/src/main/assembly/isisfish-log4j2.xml =================================================================== --- branches/4.3.0-log4j2/src/main/assembly/isisfish-log4j2.xml (rev 0) +++ branches/4.3.0-log4j2/src/main/assembly/isisfish-log4j2.xml 2014-08-28 15:52:19 UTC (rev 4102) @@ -0,0 +1,77 @@ +<?xml version="1.0" encoding="UTF-8"?> + + + +<Configuration packages="fr.ifremer.isisfish.logging" strict="true"> + + <Filters> + <SimulationThresholdFilter onMatch="ACCEPT" onMismatch="NEUTRAL" /> + </Filters> + + <Appenders> + + <Console name="Console" target="SYSTEM_OUT"> + <PatternLayout pattern="%5p [%t] (%F:%L) %M - %m%n" /> + </Console> + + <Routing name="SimulationSpecificAppender"> + <Routes pattern="$${ctx:simulationId}"> + +  + <Route key="${ctx:simulationId}"> + <Null name="Null" /> + </Route> + +  + <Route> + <File name="SimulationFileAppender-${ctx:simulationId}" fileName="${ctx:simulationLogFile}"> + <PatternLayout> + <Pattern>%p|%d{ABSOLUTE}|%F|%L|%M|%m%n</Pattern> + </PatternLayout> + </File> + </Route> + </Routes> + </Routing> + </Appenders> + + <Loggers> + <Logger name="fr.ifremer.isisfish" level="info"/> + <Logger name="org.nuiton" level="warn"/> + <Logger name="exports" level="info"/> + <Logger name="formules" level="info"/> + <Logger name="objectives" level="info"/> + <Logger name="optimizations" level="info"/> + <Logger name="rules" level="info"/> + <Logger name="scripts" level="info"/> + <Logger name="sensitivityanalysis" level="info"/> + <Logger name="sensitivityexports" level="info"/> + <Logger name="simulationplans" level="info"/> + <Logger name="simulators" level="info"/> + + <Root level="error"> + <AppenderRef ref="Console" /> + <AppenderRef ref="SimulationSpecificAppender" /> + </Root> + </Loggers> +</Configuration> \ No newline at end of file Property changes on: branches/4.3.0-log4j2/src/main/assembly/isisfish-log4j2.xml ___________________________________________________________________ Added: svn:mime-type + text/xml Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native Modified: branches/4.3.0-log4j2/src/main/assembly/isisfish.bat =================================================================== --- branches/4.3.0-log4j2/src/main/assembly/isisfish.bat 2014-08-28 14:25:25 UTC (rev 4101) +++ branches/4.3.0-log4j2/src/main/assembly/isisfish.bat 2014-08-28 15:52:19 UTC (rev 4102) @@ -1,8 +1,8 @@ @echo off rem Uncomment following 2 lines to easy configure R for ISIS-Fish -rem SET R_HOME=C:\Program Files\R\R-3.0.0 +rem SET R_HOME=C:\Program Files\R\R-3.1.0 rem SET PATH=%PATH%;%R_HOME%\bin\i386 echo [Script] Isis starting... -java -Xmx900M -jar ${project.build.finalName}.${project.packaging} %1 %2 %3 %4 %5 %6 %7 %8 %9 > debug.txt 2>&1 +java -Xmx2048M -jar ${project.build.finalName}.${project.packaging} %1 %2 %3 %4 %5 %6 %7 %8 %9 > debug.txt 2>&1 Modified: branches/4.3.0-log4j2/src/main/assembly/isisfish.sh =================================================================== --- branches/4.3.0-log4j2/src/main/assembly/isisfish.sh 2014-08-28 14:25:25 UTC (rev 4101) +++ branches/4.3.0-log4j2/src/main/assembly/isisfish.sh 2014-08-28 15:52:19 UTC (rev 4102) @@ -1,5 +1,5 @@ #!/bin/bash -MEMORY="-Xmx1024M" +MEMORY="-Xmx2048M" java $MEMORY -jar ${project.build.finalName}.${project.packaging} $* &> debug.txt

1 0

r4101 - in branches/4.3.0-log4j2: . src/main/assembly src/main/java/fr/ifremer/isisfish src/main/java/fr/ifremer/isisfish/util src/test/java/fr/ifremer/isisfish
by echatellier＠users.forge.codelutin.com 28 Aug '14

28 Aug '14

Author: echatellier Date: 2014-08-28 16:25:25 +0200 (Thu, 28 Aug 2014) New Revision: 4101 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4101 Log: Use jri installed by R with rJava R package. Added: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/RUtil.java Modified: branches/4.3.0-log4j2/pom.xml branches/4.3.0-log4j2/src/main/assembly/isisfish.bat branches/4.3.0-log4j2/src/main/assembly/isisfish.sh branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/IsisFish.java branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/JavadocHelper.java branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/AbstractIsisFishTest.java Modified: branches/4.3.0-log4j2/pom.xml =================================================================== --- branches/4.3.0-log4j2/pom.xml 2014-08-27 14:00:36 UTC (rev 4100) +++ branches/4.3.0-log4j2/pom.xml 2014-08-28 14:25:25 UTC (rev 4101) @@ -66,7 +66,15 @@ <scope>compile</scope> </dependency> +  <dependency> + <groupId>org.jboss.logging</groupId> + <artifactId>jboss-logging</artifactId> + <version>3.2.0.Beta1</version> + <scope>runtime</scope> + </dependency> + + <dependency> <groupId>org.nuiton</groupId> <artifactId>nuiton-profiling</artifactId> <version>3.0</version> Modified: branches/4.3.0-log4j2/src/main/assembly/isisfish.bat =================================================================== --- branches/4.3.0-log4j2/src/main/assembly/isisfish.bat 2014-08-27 14:00:36 UTC (rev 4100) +++ branches/4.3.0-log4j2/src/main/assembly/isisfish.bat 2014-08-28 14:25:25 UTC (rev 4101) @@ -5,4 +5,4 @@ rem SET PATH=%PATH%;%R_HOME%\bin\i386 echo [Script] Isis starting... -java -Xmx900M -Djri.load.classpath.libs=true -jar ${project.build.finalName}.${project.packaging} %1 %2 %3 %4 %5 %6 %7 %8 %9 > debug.txt 2>&1 +java -Xmx900M -jar ${project.build.finalName}.${project.packaging} %1 %2 %3 %4 %5 %6 %7 %8 %9 > debug.txt 2>&1 Modified: branches/4.3.0-log4j2/src/main/assembly/isisfish.sh =================================================================== --- branches/4.3.0-log4j2/src/main/assembly/isisfish.sh 2014-08-27 14:00:36 UTC (rev 4100) +++ branches/4.3.0-log4j2/src/main/assembly/isisfish.sh 2014-08-28 14:25:25 UTC (rev 4101) @@ -2,4 +2,4 @@ MEMORY="-Xmx1024M" -java $MEMORY -Djri.load.classpath.libs=true -jar ${project.build.finalName}.${project.packaging} $* &> debug.txt +java $MEMORY -jar ${project.build.finalName}.${project.packaging} $* &> debug.txt Modified: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/IsisFish.java =================================================================== --- branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/IsisFish.java 2014-08-27 14:00:36 UTC (rev 4100) +++ branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/IsisFish.java 2014-08-28 14:25:25 UTC (rev 4101) @@ -83,6 +83,7 @@ import fr.ifremer.isisfish.ui.util.ErrorHelper; import fr.ifremer.isisfish.util.IsisCache; import fr.ifremer.isisfish.util.IsisMatrixSemanticMapper; +import fr.ifremer.isisfish.util.RUtil; import fr.ifremer.isisfish.vcs.VCS; import fr.ifremer.isisfish.vcs.VCSActionEvent; import fr.ifremer.isisfish.vcs.VCSException; @@ -120,16 +121,10 @@ } public static void main(String... args) throws Exception { - - // TODO as of 20140720, hibernate fails to detect log4j 2.0, force slf4j - System.setProperty("org.jboss.logging.provider", "slf4j"); - + // permet de faire fonctionner la compilation en webstart System.setSecurityManager(null); - // set Rtype in jni mode - System.setProperty("R.type", "jni"); - // initialisation de l'application init(args); @@ -143,6 +138,9 @@ log.info("PATH: " + System.getenv("PATH")); } + // init R way for isis + RUtil.initJri(); + // action after init config.doAction(IsisConfig.STEP_AFTER_INIT); Modified: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/JavadocHelper.java =================================================================== --- branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/JavadocHelper.java 2014-08-27 14:00:36 UTC (rev 4100) +++ branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/JavadocHelper.java 2014-08-28 14:25:25 UTC (rev 4101) @@ -39,7 +39,6 @@ import java.util.List; import org.apache.commons.io.FileUtils; -import org.apache.commons.lang3.reflect.MethodUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.nuiton.util.FileUtil; Added: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/RUtil.java =================================================================== --- branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/RUtil.java (rev 0) +++ branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/RUtil.java 2014-08-28 14:25:25 UTC (rev 4101) @@ -0,0 +1,137 @@ +/* + * #%L + * IsisFish + * + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2006 - 2012 Ifremer, Code Lutin, Cédric Pineau, Benjamin Poussin, Chatellier Eric + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 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; + +import java.io.File; +import java.io.IOException; +import java.io.InputStream; +import java.lang.reflect.Field; +import java.util.List; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +/** + * Utility class fo R integration with isis fish. + * + * @author Eric Chatellier + */ +public class RUtil { + + private static final Log log = LogFactory.getLog(RUtil.class); + + /** + * Try to call "R" process to get location where jri is installed. + */ + public static void initJri() { + + // set Rtype in jni mode + System.setProperty("R.type", "jni"); + + try { + ProcessBuilder pb = new ProcessBuilder("Rscript", "-e", "installed.packages()[which(installed.packages()[,1]=='rJava'),]['LibPath']"); + Process process = pb.start(); + int exitValue = process.waitFor(); + + if (exitValue == 0) { + // normal exit + parseRscriptOutput(process.getInputStream()); + } else { + // R trouvé, mais la commande R a échoué + InputStream err = process.getErrorStream(); + if (log.isErrorEnabled()) { + log.error("Can't call Rscript : " + IOUtils.toString(err)); + } + } + } catch (IOException ex) { + // Le processus n'a pas pu être lancé (R non trouvé) + if (log.isDebugEnabled()) { + log.debug("Can't find R", ex); + } + } catch (InterruptedException ex) { + if (log.isErrorEnabled()) { + log.error("Can't find R", ex); + } + } + } + + /** + * Parse valid Rscript output to find if rJava is installed and where it is installed. + * + * @param is process output + * @throws IOException + */ + protected static void parseRscriptOutput(InputStream is) throws IOException { + List<String> output = IOUtils.readLines(is); + + // 1 lignes = commande OK, mais rJava n'est pas installé + // 2 lignes = commande OK et rJava est installé + if (output.size() == 1) { + //installRJava(); + } else if (output.size() == 2) { + // get install location without "" + String location = output.get(1).trim(); + location = StringUtils.removeStart(location, "\""); + location = StringUtils.removeEnd(location, "\""); + // build full library path + location = location.replace('/', File.separatorChar); + location += File.separator + "rJava" + File.separator + "jri"; + setJavaLibraryPath(location); + } else if (log.isErrorEnabled()) { + log.error("Can't analyze Rscript output. was: "); + for (String line : output) { + log.error(line); + } + } + } + + /** + * Set runtime java library path. + * + * http://fahdshariff.blogspot.fr/2011/08/changing-java-library-path-at-runtim… + * + * @param newValue new value to set + */ + protected static void setJavaLibraryPath(String newValue) { + if (log.isInfoEnabled()) { + log.info("Adding '" + newValue + "' to java.library.path"); + } + System.setProperty("java.library.path", newValue); + + //set sys_paths to null + try { + final Field sysPathsField = ClassLoader.class.getDeclaredField("sys_paths"); + sysPathsField.setAccessible(true); + sysPathsField.set(null, null); + } catch (NoSuchFieldException | IllegalArgumentException | IllegalAccessException ex) { + if (log.isErrorEnabled()) { + log.error("Cant' reset ClassLoader#sys_paths value", ex); + } + } + } +} Property changes on: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/util/RUtil.java ___________________________________________________________________ Added: svn:eol-style + native Added: svn:keywords + Author Date Id Revision HeadURL Modified: branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/AbstractIsisFishTest.java =================================================================== --- branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/AbstractIsisFishTest.java 2014-08-27 14:00:36 UTC (rev 4100) +++ branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/AbstractIsisFishTest.java 2014-08-28 14:25:25 UTC (rev 4101) @@ -86,9 +86,6 @@ @BeforeClass public static void init() throws Exception { - // TODO as of 20140720, hibernate fails to detect log4j 2.0, force slf4j - System.setProperty("org.jboss.logging.provider", "slf4j"); - File mavenTestDir = getTestDirectory(); dirIsisBase = FileUtil.createTempDirectory("isisdbtest", "", mavenTestDir);

1 0

r4100 - in branches/4.3.0-log4j2: . src/main/java/fr/ifremer/isisfish src/main/java/fr/ifremer/isisfish/datastore src/main/java/fr/ifremer/isisfish/vcs src/main/resources src/test/java/fr/ifremer/isisfish/vcs
by echatellier＠users.forge.codelutin.com 27 Aug '14

27 Aug '14

Author: echatellier Date: 2014-08-27 16:00:36 +0200 (Wed, 27 Aug 2014) New Revision: 4100 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4100 Log: fixes #5688: Extract static version to properties file Added: branches/4.3.0-log4j2/src/main/resources/isis-config-4 Modified: branches/4.3.0-log4j2/pom.xml branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/IsisConfig.java branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/IsisFish.java branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/datastore/VersionStorage.java branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/vcs/VCS.java branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/vcs/VCSNone.java branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/vcs/VCSSVN.java branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/vcs/VCSSVNTest.java Modified: branches/4.3.0-log4j2/pom.xml =================================================================== --- branches/4.3.0-log4j2/pom.xml 2014-08-27 13:06:43 UTC (rev 4099) +++ branches/4.3.0-log4j2/pom.xml 2014-08-27 14:00:36 UTC (rev 4100) @@ -20,7 +20,7 @@ <dependency> <groupId>org.nuiton</groupId> <artifactId>nuiton-utils</artifactId> - <version>3.0-rc-7</version> + <version>3.0-SNAPSHOT</version> <scope>compile</scope> </dependency> @@ -514,6 +514,23 @@ </distributionManagement> <build> + <resources> + <resource> + <directory>src/main/resources</directory> + <includes> + <include>isis-config-4</include> + </includes> + <filtering>true</filtering> + </resource> + <resource> + <directory>src/main/resources</directory> + <excludes> + <exclude>isis-config-4</exclude> + </excludes> + <filtering>false</filtering> + </resource> + </resources> + <pluginManagement> <plugins> <plugin> Modified: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-08-27 13:06:43 UTC (rev 4099) +++ branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-08-27 14:00:36 UTC (rev 4100) @@ -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 @@ -45,12 +45,13 @@ import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.nuiton.config.ApplicationConfig; +import org.nuiton.config.ArgumentsParserException; import org.nuiton.config.ConfigOptionDef; -import org.nuiton.converter.ConverterUtil; import org.nuiton.math.matrix.DoubleBigVector; import org.nuiton.math.matrix.DoubleSparseHashVector; import org.nuiton.util.StringUtil; -import org.nuiton.util.Version; +import org.nuiton.util.version.Version; +import org.nuiton.util.version.Versions; import fr.ifremer.isisfish.actions.ExportAction; import fr.ifremer.isisfish.actions.ImportAction; @@ -82,6 +83,9 @@ /** Class logger. */ static private Log log = LogFactory.getLog(IsisConfig.class); + /** Numero de version majeure d'isis fish. */ + public static final int ISIS_FISH_MAJOR_VERSION = 4; + /** * Config step after init. * @@ -128,18 +132,10 @@ * migration de donnees demande automatiquement un changement de version * d'application. */ - protected final static Version version = new Version(4, 3, 2, 0); + protected static Version version; + protected static Version databaseVersion; + protected static Version apiVersion; - protected final static Version majorVersion = new Version(version.getNumber(0)); - protected final static Version databaseVersion = new Version( - version.getNumber(0), version.getNumber(1)); - protected final static Version apiVersion = new Version( - version.getNumber(0), version.getNumber(1), version.getNumber(2)); - - public static Version getVersionNumber() { - return version; - } - /** * Le nombre global ex: 3.2.0.0 * @@ -168,9 +164,6 @@ return apiVersion; } - static final public String COPYRIGHT_TEXT = "Version " + getVersion() + " IFREMER-MAERHA © 2000-2014"; - static final public String CONFIG_FILENAME = "isis-config-" + majorVersion.toString(); - /** separateur de liste */ static final public String SEP = ","; @@ -200,6 +193,26 @@ } } } + + @Override + public ApplicationConfig parse(String... args) throws ArgumentsParserException { + ApplicationConfig config = super.parse(args); + postInitWithVersion(config.getOption("isisfish.version")); + return config; + } + + /** + * Initialize avec des valeurs par defaut des options dans la valeur dépend de la version. + * + * @param fullVersion full version (ex 4.3.1.9) + */ + protected void postInitWithVersion(String fullVersion) { + IsisConfig.version = Versions.valueOf(fullVersion); + IsisConfig.databaseVersion = Versions.extractVersion(IsisConfig.version, 0, 1); + IsisConfig.apiVersion = Versions.extractVersion(IsisConfig.version, 0, 2); + + setDefaultOption(Option.SIMULATOR_SSH_ISIS_HOME.key, "/home3/caparmor/poussin/isis-fish-" + apiVersion.toString()); + } ////////////////////////////////////////////////// // Methode d'acces aux options @@ -1078,8 +1091,8 @@ */ public static enum Option implements ConfigOptionDef { - CONFIG_FILE(CONFIG_FILE_NAME, n("isisfish.config.main.configFileName.description"), CONFIG_FILENAME), - ISIS_HOME_DIRECTORY("isis.home.directory", n("isisfish.config.main.compileDirectory.description"), getUserHome() + File.separator + "isis-fish-" + majorVersion.toString()), + CONFIG_FILE(CONFIG_FILE_NAME, n("isisfish.config.main.configFileName.description"), "isis-config-" + ISIS_FISH_MAJOR_VERSION), + ISIS_HOME_DIRECTORY("isis.home.directory", n("isisfish.config.main.compileDirectory.description"), getUserHome() + File.separator + "isis-fish-" + ISIS_FISH_MAJOR_VERSION), COMPILATION_DIRECTORY("compilation.directory", n("isisfish.config.main.compileDirectory.description"), "${isis.home.directory}" + File.separator + "isis-build"), MONITORING_DIRECTORY("monitoring.directory", n("isisfish.config.main.monitoringDirectory.description"), "${isis.home.directory}" + File.separator + "isis-monitoring"), JAVADOC_DIRECTORY("javadoc.directory", n("isisfish.config.main.javadocDirectory.description"), "${isis.home.directory}" + File.separator + "isis-docs"), @@ -1122,9 +1135,9 @@ /** Serveur accessible par ssh : user home directory */ SIMULATOR_SSH_USER_HOME("simulation.ssh.userhome", n("isisfish.config.main.simulation.ssh.userhome.description"), ""), /** Serveur accessible par ssh : remote data path */ - SIMULATOR_SSH_DATAPATH("simulation.ssh.datapath", n("isisfish.config.main.simulation.ssh.datapath.description"), "isis-fish-" + majorVersion.toString() + "/isis-database"), + SIMULATOR_SSH_DATAPATH("simulation.ssh.datapath", n("isisfish.config.main.simulation.ssh.datapath.description"), "isis-fish-4/isis-database"), /** Serveur accessible par ssh : remote isis home install */ - SIMULATOR_SSH_ISIS_HOME("simulation.ssh.isis.home", n("isisfish.config.main.simulation.ssh.isis.home.description"), "/home3/caparmor/poussin/isis-fish-" + IsisConfig.getApiVersion()), + SIMULATOR_SSH_ISIS_HOME("simulation.ssh.isis.home", n("isisfish.config.main.simulation.ssh.isis.home.description"), null), /** Serveur accessible par ssh : remote tmp path */ SIMULATOR_SSH_TMPPATH("simulation.ssh.tmppath", n("isisfish.config.main.simulation.ssh.tmppath.description"), "isis-tmp"), /** Serveur accessible par SSH : emplacement de Java (full path) */ Modified: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/IsisFish.java =================================================================== --- branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/IsisFish.java 2014-08-27 13:06:43 UTC (rev 4099) +++ branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/IsisFish.java 2014-08-27 14:00:36 UTC (rev 4100) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2005 - 2013 Ifremer, CodeLutin, Chatellier Eric + * Copyright (C) 2005 - 2014 Ifremer, CodeLutin, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -58,7 +58,7 @@ import org.nuiton.i18n.init.DefaultI18nInitializer; import org.nuiton.math.matrix.MatrixFactory; import org.nuiton.topia.TopiaException; -import org.nuiton.util.Version; +import org.nuiton.util.version.Version; import org.nuiton.widget.SwingSession; import com.bbn.openmap.MapBean; @@ -130,6 +130,9 @@ // set Rtype in jni mode System.setProperty("R.type", "jni"); + // initialisation de l'application + init(args); + // i18n is not inited here if (log.isInfoEnabled()) { log.info("Starting Isis-Fish " + IsisConfig.getVersion() + " with args : " + java.util.Arrays.toString(args)); @@ -140,13 +143,6 @@ log.info("PATH: " + System.getenv("PATH")); } - // initialisation de l'application - init(args); - - if (log.isDebugEnabled()) { - log.debug(t("isisfish.launch.init.done", config.getElapsedTimeAsString())); - } - // action after init config.doAction(IsisConfig.STEP_AFTER_INIT); @@ -181,6 +177,13 @@ } /** + * Initialize isis fish version from properties files. + */ + protected static void initVersion() { + + } + + /** * Start cron service (if enabled). */ protected static void startCronService() { @@ -256,6 +259,10 @@ // after init shutdown hook Runtime.getRuntime().addShutdownHook(new IsisQuitHook()); + + if (log.isDebugEnabled()) { + log.debug(t("isisfish.launch.init.done", config.getElapsedTimeAsString())); + } } /** Modified: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/datastore/VersionStorage.java =================================================================== --- branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/datastore/VersionStorage.java 2014-08-27 13:06:43 UTC (rev 4099) +++ branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/datastore/VersionStorage.java 2014-08-27 14:00:36 UTC (rev 4100) @@ -37,7 +37,7 @@ import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.nuiton.util.ListenerSet; -import org.nuiton.util.Version; +import org.nuiton.util.version.Version; import fr.ifremer.isisfish.IsisConfig; import fr.ifremer.isisfish.IsisFish; Modified: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/vcs/VCS.java =================================================================== --- branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/vcs/VCS.java 2014-08-27 13:06:43 UTC (rev 4099) +++ branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/vcs/VCS.java 2014-08-27 14:00:36 UTC (rev 4100) @@ -30,7 +30,7 @@ import java.util.List; import java.util.Map; -import org.nuiton.util.Version; +import org.nuiton.util.version.Version; /** * Version control system. Modified: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/vcs/VCSNone.java =================================================================== --- branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/vcs/VCSNone.java 2014-08-27 13:06:43 UTC (rev 4099) +++ branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/vcs/VCSNone.java 2014-08-27 14:00:36 UTC (rev 4100) @@ -31,7 +31,7 @@ import java.util.List; import java.util.Map; -import org.nuiton.util.Version; +import org.nuiton.util.version.Version; /** * VCSNone (svn or vcs) must extends this class. This class can be used as dummy Modified: branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/vcs/VCSSVN.java =================================================================== --- branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/vcs/VCSSVN.java 2014-08-27 13:06:43 UTC (rev 4099) +++ branches/4.3.0-log4j2/src/main/java/fr/ifremer/isisfish/vcs/VCSSVN.java 2014-08-27 14:00:36 UTC (rev 4100) @@ -40,7 +40,7 @@ import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.nuiton.util.Version; +import org.nuiton.util.version.Version; import org.tmatesoft.svn.core.ISVNDirEntryHandler; import org.tmatesoft.svn.core.ISVNLogEntryHandler; import org.tmatesoft.svn.core.SVNCommitInfo; Added: branches/4.3.0-log4j2/src/main/resources/isis-config-4 =================================================================== --- branches/4.3.0-log4j2/src/main/resources/isis-config-4 (rev 0) +++ branches/4.3.0-log4j2/src/main/resources/isis-config-4 2014-08-27 14:00:36 UTC (rev 4100) @@ -0,0 +1 @@ +isisfish.version=${project.version} Modified: branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/vcs/VCSSVNTest.java =================================================================== --- branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/vcs/VCSSVNTest.java 2014-08-27 13:06:43 UTC (rev 4099) +++ branches/4.3.0-log4j2/src/test/java/fr/ifremer/isisfish/vcs/VCSSVNTest.java 2014-08-27 14:00:36 UTC (rev 4100) @@ -37,7 +37,8 @@ import org.apache.commons.io.FileUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.nuiton.util.Version; +import org.nuiton.util.version.Version; +import org.nuiton.util.version.Versions; import org.junit.After; import org.junit.Assert; import org.junit.Before; @@ -326,7 +327,7 @@ vcs.add(Arrays.asList(fileToAdd), "ajout d'un fichier"); // test switchTag - vcs.setTag(new Version(3, 1, 0)); + vcs.setTag(Versions.valueOf("3.1.0")); Assert.assertTrue(vcs.getTag().startsWith("/tags/3.1.0")); Assert.assertEquals(FILECONTENTTAG, FileUtils.readFileToString(version)); Assert.assertTrue(demo.exists()); @@ -890,10 +891,10 @@ log.info("testGetDiff()"); } - Version version = new Version(3, 1, 0); + Version version = Versions.valueOf("3.1.0"); Assert.assertTrue(vcs.isTag(version)); - version = new Version(3, 2, 0); + version = Versions.valueOf("3.2.0"); Assert.assertFalse(vcs.isTag(version)); } @@ -1144,7 +1145,7 @@ } // chechout tags - vcs.checkout(new Version(3, 1, 0), false); + vcs.checkout(Versions.valueOf("3.1.0"), false); // modif on remote repo on tag :) File file = new File(vcs.getLocalRepository(), "scripts" @@ -1173,7 +1174,7 @@ FileUtils.writeStringToFile(file2, "oooooo"); // try to update... - List<File> filesInConflict = vcs.setTag(new Version(3, 1, 0)); + List<File> filesInConflict = vcs.setTag(Versions.valueOf("3.1.0")); Assert.assertNotNull(filesInConflict); Assert.assertEquals(1, filesInConflict.size()); log.debug("Conflicts are : " + filesInConflict);

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r4099 - branches/4.3.0-log4j2
by echatellier＠users.forge.codelutin.com 27 Aug '14

27 Aug '14

Author: echatellier Date: 2014-08-27 15:06:43 +0200 (Wed, 27 Aug 2014) New Revision: 4099 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4099 Log: Update libs Modified: branches/4.3.0-log4j2/pom.xml Modified: branches/4.3.0-log4j2/pom.xml =================================================================== --- branches/4.3.0-log4j2/pom.xml 2014-08-21 15:44:13 UTC (rev 4098) +++ branches/4.3.0-log4j2/pom.xml 2014-08-27 13:06:43 UTC (rev 4099) @@ -20,16 +20,9 @@ <dependency> <groupId>org.nuiton</groupId> <artifactId>nuiton-utils</artifactId> - <version>3.0-rc-6</version> + <version>3.0-rc-7</version> <scope>compile</scope> </dependency> - -  <dependency> <groupId>org.nuiton</groupId> @@ -311,7 +304,7 @@  <dependency> - <groupId>ssj</groupId> + <groupId>ca.umontreal.iro</groupId> <artifactId>ssj</artifactId> <version>2.5</version> <scope>runtime</scope> @@ -343,7 +336,7 @@ <dependency> <groupId>com.google.guava</groupId> <artifactId>guava</artifactId> - <version>17.0</version> + <version>18.0</version> </dependency>  @@ -492,7 +485,7 @@ <signatureVersion>1.0</signatureVersion>  - <jaxxVersion>2.10</jaxxVersion> + <jaxxVersion>2.11</jaxxVersion> <eugeneVersion>2.13</eugeneVersion> <topiaVersion>2.9.2</topiaVersion> <hibernateVersion>4.3.6.Final</hibernateVersion>

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