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r3828 - branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain
by echatellier＠users.forge.codelutin.com Nov. 2, 2013

Nov. 2, 2013

Author: echatellier Date: 2013-11-02 11:13:56 +0100 (Sat, 02 Nov 2013) New Revision: 3828 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3828 Log: Add missing getDistribution parameter method Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java 2013-11-02 09:51:05 UTC (rev 3827) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java 2013-11-02 10:13:56 UTC (rev 3828) @@ -103,6 +103,16 @@ } /** + * Return distribution parameter value by parameter name. + * + * @param name name + * @return param value + */ + public Object getDistributionParameter(String name) { + return distributionParameters.get(name); + } + + /** * Set distribution parameters (clear previous). * * @param distributionParameters distribution params

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r3827 - in branches/4.0.1: . src/main/java/fr/ifremer/isisfish/datastore src/main/java/fr/ifremer/isisfish/entities src/main/java/fr/ifremer/isisfish/simulator/launcher src/main/resources/i18n
by echatellier＠users.forge.codelutin.com Nov. 2, 2013

Nov. 2, 2013

Author: echatellier Date: 2013-11-02 10:51:05 +0100 (Sat, 02 Nov 2013) New Revision: 3827 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3827 Log: Fix some reported problems Modified: branches/4.0.1/pom.xml branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/CodeSourceStorage.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/entities/PopulationImpl.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/entities/SeasonImpl.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java branches/4.0.1/src/main/resources/i18n/isis-fish_en_GB.properties branches/4.0.1/src/main/resources/i18n/isis-fish_fr_FR.properties Modified: branches/4.0.1/pom.xml =================================================================== --- branches/4.0.1/pom.xml 2013-11-02 09:31:48 UTC (rev 3826) +++ branches/4.0.1/pom.xml 2013-11-02 09:51:05 UTC (rev 3827) @@ -295,17 +295,17 @@ <dependency> <groupId>org.aspectj</groupId> <artifactId>aspectjrt</artifactId> - <version>1.7.3</version> + <version>1.7.4</version> </dependency> <dependency> <groupId>org.aspectj</groupId> <artifactId>aspectjweaver</artifactId> - <version>1.7.3</version> + <version>1.7.4</version> </dependency> <dependency> <groupId>org.aspectj</groupId> <artifactId>aspectjtools</artifactId> - <version>1.7.3</version> + <version>1.7.4</version> </dependency>  @@ -321,7 +321,7 @@ <dependency> <groupId>org.tmatesoft.svnkit</groupId> <artifactId>svnkit</artifactId> - <version>1.8.0-SNAPSHOT</version> + <version>1.7.8</version> <scope>compile</scope> </dependency>  @@ -476,7 +476,7 @@ <signatureVersion>1.0</signatureVersion>  - <jaxxVersion>2.5.28</jaxxVersion> + <jaxxVersion>2.5.29</jaxxVersion> <eugeneVersion>2.6.3</eugeneVersion> <topiaVersion>2.8.1.3</topiaVersion> <hibernateVersion>4.2.7.Final</hibernateVersion> @@ -679,10 +679,6 @@ <id>nuiton.public</id> <url>http://nexus.nuiton.org/nexus/content/groups/public</url> </repository> - <repository> - <id>svnkit.public</id> - <url>http://maven.tmatesoft.com/content/repositories/snapshots</url> - </repository> </repositories> <pluginRepositories> @@ -741,7 +737,7 @@ <properties>  <minimumTokens>100</minimumTokens> - <targetJdk>1.6</targetJdk> + <targetJdk>1.7</targetJdk> </properties> <build> Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/CodeSourceStorage.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/CodeSourceStorage.java 2013-11-02 09:31:48 UTC (rev 3826) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/CodeSourceStorage.java 2013-11-02 09:51:05 UTC (rev 3827) @@ -31,7 +31,6 @@ import java.util.List; import org.apache.commons.io.FileUtils; -import org.nuiton.util.FileUtil; import fr.ifremer.isisfish.IsisFish; import fr.ifremer.isisfish.IsisFishRuntimeException; Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/entities/PopulationImpl.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/entities/PopulationImpl.java 2013-11-02 09:31:48 UTC (rev 3826) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/entities/PopulationImpl.java 2013-11-02 09:51:05 UTC (rev 3827) @@ -559,8 +559,6 @@ // matrix when capturability is null instead check validity and // create new one and paste the old } else if (!Arrays.equals(mat.getSemantics(), sems)) { - log.debug("Capturability has changed, create new matrix and copy old: " - + mat.getSemantics() + " " + sems); MatrixND newmat = MatrixFactory.getInstance().create( n_("isisfish.population.capturability"), sems, Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/entities/SeasonImpl.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/entities/SeasonImpl.java 2013-11-02 09:31:48 UTC (rev 3826) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/entities/SeasonImpl.java 2013-11-02 09:51:05 UTC (rev 3827) @@ -62,7 +62,7 @@ public List<Month> getMonths() { List<Month> result = new ArrayList<Month>(); Month m = getFirstMonth(); - while (m.equals(getLastMonth()) == false) { + while (!m.equals(getLastMonth())) { result.add(m); m = m.next(); } @@ -92,7 +92,7 @@ boolean result = month.equals(getLastMonth()); // check first last month, because loop don't do that Month m = getFirstMonth(); - while (result == false && m.equals(getLastMonth()) == false) { + while (!result && !m.equals(getLastMonth())) { result = m.equals(month); m = m.next(); } Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java 2013-11-02 09:31:48 UTC (rev 3826) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java 2013-11-02 09:51:05 UTC (rev 3827) @@ -425,7 +425,7 @@ waitAndCheckProgression(); } catch (Exception e) { if (log.isErrorEnabled()) { - log.error("An exception occurs durring monitoring", e); + log.error("An exception occurs during monitoring", e); } } } Modified: branches/4.0.1/src/main/resources/i18n/isis-fish_en_GB.properties =================================================================== --- branches/4.0.1/src/main/resources/i18n/isis-fish_en_GB.properties 2013-11-02 09:31:48 UTC (rev 3826) +++ branches/4.0.1/src/main/resources/i18n/isis-fish_en_GB.properties 2013-11-02 09:51:05 UTC (rev 3827) @@ -1,4 +1,6 @@ = +%s\ has\ a\ discrete\ domain,\ this\ is\ not\ acceptable\ for\ this\ method.= +%s\ has\ a\ non\ uniform\ distribution,\ this\ is\ not\ acceptable\ for\ this\ method.= Add\ to\ default\ queue= Analyse\ plan\ error,\ too\ many\ simulation\ for\ %s\ \:\ %s= Can't\ add\ result\ '%1$s'\ at\ date\ %2$s=Can't add result '%1$s' at date %2$s @@ -39,12 +41,14 @@ Maximum\ value= Minimum\ value= Missing\ name= +Modifier\ le\ code\ R\ envoyé\ si\ vous\ le\ souhaitez= No\ port\ cell= Normal\ stop\ thread,\ this\ is\ not\ an\ error= Not\ start\ simulation\ %s\ because\ user\ ask\ stop= Process\ template\ error= QUnif\ %= QUnif\ Min/Max= +R\ modif= Reference\ value= Region\ %s\ allready\ exist\ in\ repository.\ Can't\ import= Region\ %s\ already\ inited= Modified: branches/4.0.1/src/main/resources/i18n/isis-fish_fr_FR.properties =================================================================== --- branches/4.0.1/src/main/resources/i18n/isis-fish_fr_FR.properties 2013-11-02 09:31:48 UTC (rev 3826) +++ branches/4.0.1/src/main/resources/i18n/isis-fish_fr_FR.properties 2013-11-02 09:51:05 UTC (rev 3827) @@ -1,4 +1,6 @@ = +%s\ has\ a\ discrete\ domain,\ this\ is\ not\ acceptable\ for\ this\ method.= +%s\ has\ a\ non\ uniform\ distribution,\ this\ is\ not\ acceptable\ for\ this\ method.= Add\ to\ default\ queue= Analyse\ plan\ error,\ too\ many\ simulation\ for\ %s\ \:\ %s= Can't\ add\ result\ '%1$s'\ at\ date\ %2$s=Can't add result '%1$s' at date %2$s @@ -39,12 +41,14 @@ Maximum\ value= Minimum\ value= Missing\ name= +Modifier\ le\ code\ R\ envoyé\ si\ vous\ le\ souhaitez= No\ port\ cell= Normal\ stop\ thread,\ this\ is\ not\ an\ error= Not\ start\ simulation\ %s\ because\ user\ ask\ stop= Process\ template\ error= QUnif\ %= QUnif\ Min/Max= +R\ modif= Reference\ value= Region\ %s\ allready\ exist\ in\ repository.\ Can't\ import= Region\ %s\ already\ inited=La région %s a déjà été initialisée

1 0

r3826 - in branches/4.0.1/src/main/java/fr/ifremer/isisfish: types/hibernate util
by echatellier＠users.forge.codelutin.com Nov. 2, 2013

Nov. 2, 2013

Author: echatellier Date: 2013-11-02 10:31:48 +0100 (Sat, 02 Nov 2013) New Revision: 3826 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3826 Log: Comment non used code non compilable since hibernate 4.2 Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/types/hibernate/MatrixType.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/TopiaEntityConverter.java Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/types/hibernate/MatrixType.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/types/hibernate/MatrixType.java 2013-10-31 22:54:54 UTC (rev 3825) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/types/hibernate/MatrixType.java 2013-11-02 09:31:48 UTC (rev 3826) @@ -69,9 +69,6 @@ */ private static final Log log = LogFactory.getLog(MatrixType.class); - public MatrixType() { - } - public boolean isMutable() { return true; } @@ -92,7 +89,7 @@ if(str.startsWith("[") && str.endsWith("]")) { str = str.substring(1, str.length()-1); // remove [ and ] } - String [] dimAsString = StringUtil.split(str, ","); + String [] dimAsString = StringUtil.split(str, ","); int[] result = new int[dimAsString.length]; int i = 0; for (String dim : dimAsString) { @@ -285,8 +282,8 @@ private static final Type[] hibernateTypes = { StandardBasicTypes.STRING, //name (String) StandardBasicTypes.STRING, //dim (int[]) - StandardBasicTypes.CLOB, //dimNames (String[]) - StandardBasicTypes.CLOB, //semantics (List[]) + StandardBasicTypes.CLOB, //dimNames (String[]) + StandardBasicTypes.CLOB, //semantics (List[]) StandardBasicTypes.CLOB //data (List<List<...>>) }; Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/TopiaEntityConverter.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/TopiaEntityConverter.java 2013-10-31 22:54:54 UTC (rev 3825) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/TopiaEntityConverter.java 2013-11-02 09:31:48 UTC (rev 3826) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2006 - 2011 Ifremer, Code Lutin, Cédric Pineau, Benjamin Poussin, Chatellier Eric + * Copyright (C) 2006 - 2013 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 @@ -32,15 +32,14 @@ import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.hibernate.HibernateException; -import org.hibernate.engine.QueryParameters; -import org.hibernate.engine.SessionImplementor; +import org.hibernate.engine.spi.QueryParameters; +import org.hibernate.engine.spi.SessionImplementor; import org.hibernate.type.StandardBasicTypes; import org.nuiton.topia.TopiaContext; import org.nuiton.topia.TopiaException; import org.nuiton.topia.persistence.TopiaEntity; import org.nuiton.topia.persistence.TopiaId; - /** * Classe utilise pour convertir une chaine en un objet TopiaEntity. * @@ -50,15 +49,12 @@ */ public class TopiaEntityConverter implements Converter { - /** - * Logger for this class - */ - private static final Log log = LogFactory - .getLog(TopiaEntityConverter.class); + /** Logger for this class. */ + private static final Log log = LogFactory.getLog(TopiaEntityConverter.class); protected TopiaContext context = null; protected SessionImplementor session = null; - + public TopiaEntityConverter(TopiaContext context) { this.context = context; } @@ -67,15 +63,13 @@ this.session = session; } - /* (non-Javadoc) - * @see org.apache.commons.beanutils.Converter#convert(java.lang.Class, java.lang.Object) - */ + @Override public Object convert(Class type, Object value) { Object result = null; if (value instanceof TopiaEntity) { result = value; - } else if (value instanceof String){ - result = getTopiaEntity((String)value); + } else if (value instanceof String) { + result = getTopiaEntity((String) value); } else { throw new ConversionException("Can't convert '" + value + "' to " + type.getName()); } @@ -88,7 +82,8 @@ try { TopiaContext tx = context.beginTransaction(); result = tx.findByTopiaId(topiaId); - // FIXME when after tx.closeContext we can continu to load object, call it here + // FIXME when after tx.closeContext we can continu to load + // object, call it here tx.commitTransaction(); tx.closeContext(); } catch (TopiaException eee) { @@ -99,19 +94,21 @@ } else if (session != null) { QueryParameters params = new QueryParameters(StandardBasicTypes.STRING, topiaId); String entityClass = TopiaId.getClassNameAsString(topiaId); - + try { + /* Non compilable code since hibernate 4.2, but not a real, not usefull boolean mustCommit = false; if (!session.getJDBCContext().getTransaction().isActive()) { mustCommit = true; session.getJDBCContext().getTransaction().begin(); - } + }*/ String hql = "from " + entityClass + " where topiaId=?"; List results = session.list(hql, params); - if (mustCommit) { + + /*if (mustCommit) { session.getJDBCContext().getTransaction().commit(); - } - result = (TopiaEntity)results.get(0); + }*/ + result = (TopiaEntity) results.get(0); } catch (HibernateException eee) { if (log.isDebugEnabled()) { log.debug("Can't find TopiaEntity: " + topiaId, eee);

1 0

r3825 - in branches/4.0.1: . src/main/assembly src/main/java/fr/ifremer/isisfish
by echatellier＠users.forge.codelutin.com Oct. 31, 2013

Oct. 31, 2013

Author: echatellier Date: 2013-10-31 23:54:54 +0100 (Thu, 31 Oct 2013) New Revision: 3825 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3825 Log: Simplify R native library loading (now it's magic) Removed: branches/4.0.1/src/main/assembly/isisfish64.bat branches/4.0.1/src/main/assembly/isisfish64.sh branches/4.0.1/src/main/assembly/x64/ branches/4.0.1/src/main/assembly/x86/ Modified: branches/4.0.1/pom.xml branches/4.0.1/src/main/assembly/bin.xml branches/4.0.1/src/main/assembly/isisfish-log4j.properties branches/4.0.1/src/main/assembly/isisfish.bat branches/4.0.1/src/main/assembly/isisfish.sh branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisFish.java Modified: branches/4.0.1/pom.xml =================================================================== --- branches/4.0.1/pom.xml 2013-10-28 17:11:18 UTC (rev 3824) +++ branches/4.0.1/pom.xml 2013-10-31 22:54:54 UTC (rev 3825) @@ -147,7 +147,7 @@ <dependency> <groupId>org.nuiton</groupId> <artifactId>nuiton-j2r</artifactId> - <version>1.0.2</version> + <version>1.1-SNAPSHOT</version> <scope>compile</scope> </dependency> Modified: branches/4.0.1/src/main/assembly/bin.xml =================================================================== --- branches/4.0.1/src/main/assembly/bin.xml 2013-10-28 17:11:18 UTC (rev 3824) +++ branches/4.0.1/src/main/assembly/bin.xml 2013-10-31 22:54:54 UTC (rev 3825) @@ -6,7 +6,7 @@ $Id$ $HeadURL$ %% - Copyright (C) 1999 - 2010 Ifremer, CodeLutin + Copyright (C) 1999 - 2013 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 @@ -31,12 +31,6 @@ <formats> <format>zip</format> </formats> -  <fileSets> <fileSet> @@ -46,12 +40,6 @@ <include>*.jar</include> </includes> </fileSet> -  <fileSet> <includes> <include>README*</include> @@ -66,8 +54,6 @@ <includes> <include>isisfish.sh</include> <include>isisfish.bat</include> - <include>isisfish64.sh</include> - <include>isisfish64.bat</include> </includes> </fileSet> <fileSet> @@ -83,21 +69,5 @@ <file> <source>target/${artifact.artifactId}-${artifact.version}.jar</source> </file> - <file> - <source>src/main/assembly/x86/jri.dll</source> - <outputDirectory>jri</outputDirectory> - </file> - <file> - <source>src/main/assembly/x86/libjri.so</source> - <outputDirectory>jri</outputDirectory> - </file> - <file> - <source>src/main/assembly/x64/jri.dll</source> - <outputDirectory>jri64</outputDirectory> - </file> - <file> - <source>src/main/assembly/x64/libjri.so</source> - <outputDirectory>jri64</outputDirectory> - </file> </files> </assembly> Modified: branches/4.0.1/src/main/assembly/isisfish-log4j.properties =================================================================== --- branches/4.0.1/src/main/assembly/isisfish-log4j.properties 2013-10-28 17:11:18 UTC (rev 3824) +++ branches/4.0.1/src/main/assembly/isisfish-log4j.properties 2013-10-31 22:54:54 UTC (rev 3825) @@ -5,7 +5,7 @@ # $Id$ # $HeadURL$ # %% -# Copyright (C) 2011 - 2012 Ifremer, CodeLutin, Chatellier Eric +# 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 Modified: branches/4.0.1/src/main/assembly/isisfish.bat =================================================================== --- branches/4.0.1/src/main/assembly/isisfish.bat 2013-10-28 17:11:18 UTC (rev 3824) +++ branches/4.0.1/src/main/assembly/isisfish.bat 2013-10-31 22:54:54 UTC (rev 3825) @@ -5,4 +5,4 @@ rem SET PATH=%PATH%;%R_HOME%\bin\i386 echo [Script] Isis starting... -java -Xmx900M -Djava.library.path=jri -DR.type=jni -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/4.0.1/src/main/assembly/isisfish.sh =================================================================== --- branches/4.0.1/src/main/assembly/isisfish.sh 2013-10-28 17:11:18 UTC (rev 3824) +++ branches/4.0.1/src/main/assembly/isisfish.sh 2013-10-31 22:54:54 UTC (rev 3825) @@ -1,6 +1,5 @@ #!/bin/bash MEMORY="-Xmx1024M" -JRIARGS="-Djava.library.path=jri -DR.type=jni" -java $MEMORY $JRIARGS -jar ${project.build.finalName}.${project.packaging} $* &> debug.txt +java $MEMORY -jar ${project.build.finalName}.${project.packaging} $* &> debug.txt Deleted: branches/4.0.1/src/main/assembly/isisfish64.bat =================================================================== --- branches/4.0.1/src/main/assembly/isisfish64.bat 2013-10-28 17:11:18 UTC (rev 3824) +++ branches/4.0.1/src/main/assembly/isisfish64.bat 2013-10-31 22:54:54 UTC (rev 3825) @@ -1,8 +0,0 @@ -@echo off - -rem Uncomment following 2 lines to easy configure R for ISIS-Fish -rem SET R_HOME=C:\Program Files\R\R-2.14.1 -rem SET PATH=%PATH%;%R_HOME%\bin\x64 - -echo [Script] Isis starting... -java -Xmx1024M -Djava.library.path=jri64 -DR.type=jni -jar ${project.build.finalName}.${project.packaging} %1 %2 %3 %4 %5 %6 %7 %8 %9 > debug.txt 2>&1 Deleted: branches/4.0.1/src/main/assembly/isisfish64.sh =================================================================== --- branches/4.0.1/src/main/assembly/isisfish64.sh 2013-10-28 17:11:18 UTC (rev 3824) +++ branches/4.0.1/src/main/assembly/isisfish64.sh 2013-10-31 22:54:54 UTC (rev 3825) @@ -1,6 +0,0 @@ -#!/bin/bash - -MEMORY="-Xmx1024M" -JRIARGS="-Djava.library.path=jri64 -DR.type=jni" - -java $MEMORY $JRIARGS -jar ${project.build.finalName}.${project.packaging} $* &> debug.txt Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisFish.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisFish.java 2013-10-28 17:11:18 UTC (rev 3824) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisFish.java 2013-10-31 22:54:54 UTC (rev 3825) @@ -119,16 +119,17 @@ // permet de faire fonctionner la compilation en webstart System.setSecurityManager(null); + // set Rtype in jni mode + System.setProperty("R.type", "jni"); + // i18n is not inited here if (log.isInfoEnabled()) { log.info("Starting Isis-Fish " + IsisConfig.getVersion() + " with args : " + java.util.Arrays.toString(args)); log.info("Date: " + SimpleDateFormat.getInstance().format(new java.util.Date())); log.info("Java version: " + System.getProperty("java.runtime.version") + ", " + System.getProperty("java.vm.name")); - log.info("System arch: " + System.getProperty("os.arch")); - log.info("R_HOME: " + System.getenv("R_HOME") + ", R.type: " + System.getProperty("R.type")); + log.info("Plaform/arch: " + System.getProperty("os.name") + "/" + System.getProperty("os.arch")); + log.info("R_HOME: " + System.getenv("R_HOME")); log.info("PATH: " + System.getenv("PATH")); - log.info("java.library.path: " + System.getProperty("java.library.path")); - } // initialisation de l'application

1 0

r3824 - branches/4.0.1
by echatellier＠users.forge.codelutin.com Oct. 28, 2013

Oct. 28, 2013

Author: echatellier Date: 2013-10-28 18:11:18 +0100 (Mon, 28 Oct 2013) New Revision: 3824 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3824 Log: Use java 7 signature Modified: branches/4.0.1/pom.xml Modified: branches/4.0.1/pom.xml =================================================================== --- branches/4.0.1/pom.xml 2013-10-28 16:58:02 UTC (rev 3823) +++ branches/4.0.1/pom.xml 2013-10-28 17:11:18 UTC (rev 3824) @@ -472,8 +472,8 @@ <license.organizationName>Ifremer, Codelutin</license.organizationName> <maven.compiler.source>1.7</maven.compiler.source> <maven.compiler.target>1.7</maven.compiler.target> - <signatureArtifactId>java16</signatureArtifactId> - <signatureVersion>1.1</signatureVersion> + <signatureArtifactId>java17</signatureArtifactId> + <signatureVersion>1.0</signatureVersion>  <jaxxVersion>2.5.28</jaxxVersion>

1 0

r3823 - in branches/4.0.1: . src/main/java/fr/ifremer/isisfish src/main/java/fr/ifremer/isisfish/actions src/main/java/fr/ifremer/isisfish/types/hibernate src/test/java/fr/ifremer/isisfish
by echatellier＠users.forge.codelutin.com Oct. 28, 2013

Oct. 28, 2013

Author: echatellier Date: 2013-10-28 17:58:02 +0100 (Mon, 28 Oct 2013) New Revision: 3823 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3823 Log: Update libs Modified: branches/4.0.1/pom.xml branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisConfig.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/actions/ExportAction.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/actions/SimulationAction.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/types/hibernate/MatrixType.java branches/4.0.1/src/test/java/fr/ifremer/isisfish/AbstractIsisFishTest.java Modified: branches/4.0.1/pom.xml =================================================================== --- branches/4.0.1/pom.xml 2013-04-08 14:55:26 UTC (rev 3822) +++ branches/4.0.1/pom.xml 2013-10-28 16:58:02 UTC (rev 3823) @@ -6,7 +6,7 @@ <parent> <groupId>org.nuiton</groupId> <artifactId>mavenpom4redmine</artifactId> - <version>3.4.9</version> + <version>4.1</version> </parent> <groupId>fr.ifremer</groupId> @@ -20,21 +20,21 @@ <dependency> <groupId>org.nuiton</groupId> <artifactId>nuiton-utils</artifactId> - <version>${nuitonUtilsVersion}</version> + <version>2.7.1</version> <scope>compile</scope> </dependency> <dependency> <groupId>org.nuiton</groupId> <artifactId>nuiton-config</artifactId> - <version>${nuitonUtilsVersion}</version> + <version>3.0-alpha-1</version> <scope>compile</scope> </dependency> <dependency> <groupId>org.nuiton</groupId> <artifactId>nuiton-validator</artifactId> - <version>${nuitonUtilsVersion}</version> + <version>3.0-alpha-2</version> <scope>compile</scope> </dependency> @@ -90,7 +90,7 @@ <dependency> <groupId>com.fifesoft</groupId> <artifactId>rsyntaxtextarea</artifactId> - <version>2.0.6</version> + <version>2.5.0</version> <scope>runtime</scope> </dependency> @@ -189,7 +189,7 @@ <dependency> <groupId>org.apache.commons</groupId> <artifactId>commons-email</artifactId> - <version>1.3.1</version> + <version>1.3.2</version> </dependency> <dependency> @@ -255,7 +255,7 @@ <dependency> <groupId>com.jcraft</groupId> <artifactId>jsch</artifactId> - <version>0.1.49</version> + <version>0.1.50</version> <scope>compile</scope> </dependency> @@ -288,32 +288,24 @@ <dependency> <groupId>com.h2database</groupId> <artifactId>h2</artifactId> - <version>1.3.171</version> + <version>1.3.174</version> <scope>compile</scope> </dependency> -  <dependency> - <groupId>com.h2database</groupId> - <artifactId>h2mig_pagestore_addon</artifactId> - <version>1.3.153</version> - <scope>runtime</scope> - </dependency> - - <dependency> <groupId>org.aspectj</groupId> <artifactId>aspectjrt</artifactId> - <version>1.7.2</version> + <version>1.7.3</version> </dependency> <dependency> <groupId>org.aspectj</groupId> <artifactId>aspectjweaver</artifactId> - <version>1.7.2</version> + <version>1.7.3</version> </dependency> <dependency> <groupId>org.aspectj</groupId> <artifactId>aspectjtools</artifactId> - <version>1.7.2</version> + <version>1.7.3</version> </dependency>  @@ -329,7 +321,7 @@ <dependency> <groupId>org.tmatesoft.svnkit</groupId> <artifactId>svnkit</artifactId> - <version>1.7.8</version> + <version>1.8.0-SNAPSHOT</version> <scope>compile</scope> </dependency>  @@ -337,7 +329,7 @@ <dependency> <groupId>org.freemarker</groupId> <artifactId>freemarker</artifactId> - <version>2.3.19</version> + <version>2.3.20</version> <scope>compile</scope> </dependency> @@ -480,14 +472,15 @@ <license.organizationName>Ifremer, Codelutin</license.organizationName> <maven.compiler.source>1.7</maven.compiler.source> <maven.compiler.target>1.7</maven.compiler.target> + <signatureArtifactId>java16</signatureArtifactId> + <signatureVersion>1.1</signatureVersion>  - <jaxxVersion>2.5.16</jaxxVersion> - <eugeneVersion>2.6.2</eugeneVersion> - <topiaVersion>2.8-SNAPSHOT</topiaVersion> - <hibernateVersion>4.2.0.Final</hibernateVersion> - <nuitonUtilsVersion>2.6.12</nuitonUtilsVersion> - <nuitonI18nVersion>2.5</nuitonI18nVersion> + <jaxxVersion>2.5.28</jaxxVersion> + <eugeneVersion>2.6.3</eugeneVersion> + <topiaVersion>2.8.1.3</topiaVersion> + <hibernateVersion>4.2.7.Final</hibernateVersion> + <nuitonI18nVersion>2.5.2</nuitonI18nVersion> <nuitonWidgetsVersion>1.1.1</nuitonWidgetsVersion> <redmine.releaseFiles>target/isis-fish-${project.version}-bin.zip</redmine.releaseFiles> @@ -686,6 +679,10 @@ <id>nuiton.public</id> <url>http://nexus.nuiton.org/nexus/content/groups/public</url> </repository> + <repository> + <id>svnkit.public</id> + <url>http://maven.tmatesoft.com/content/repositories/snapshots</url> + </repository> </repositories> <pluginRepositories> @@ -757,7 +754,7 @@ <artifactId>maven-javadoc-plugin</artifactId> <configuration> <links> - <link>http://download.oracle.com/javase/6/docs/api/</link> + <link>http://docs.oracle.com/javase/7/docs/api/</link> <link>http://maven-site.nuiton.org/nuiton-utils/nuiton-utils/apidocs/</link> <link>http://maven-site.nuiton.org/nuiton-matrix/nuiton-matrix/apidocs/</link> <link>http://maven-site.nuiton.org/nuiton-j2r/apidocs/</link> Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2013-04-08 14:55:26 UTC (rev 3822) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2013-10-28 16:58:02 UTC (rev 3823) @@ -43,8 +43,8 @@ import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.lang3.time.DurationFormatUtils; import org.nuiton.math.matrix.DoubleBigVector; -import org.nuiton.util.config.ApplicationConfig; -import org.nuiton.util.config.ConfigOptionDef; +import org.nuiton.config.ApplicationConfig; +import org.nuiton.config.ConfigOptionDef; import org.nuiton.util.StringUtil; import org.nuiton.util.Version; Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/actions/ExportAction.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/actions/ExportAction.java 2013-04-08 14:55:26 UTC (rev 3822) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/actions/ExportAction.java 2013-10-28 16:58:02 UTC (rev 3823) @@ -36,7 +36,7 @@ import org.apache.commons.io.FileUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.nuiton.util.ApplicationConfig.Action.Step; +import org.nuiton.config.ApplicationConfig.Action.Step; import fr.ifremer.isisfish.IsisConfig; import fr.ifremer.isisfish.datastore.SimulationPlanStorage; Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/actions/SimulationAction.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/actions/SimulationAction.java 2013-04-08 14:55:26 UTC (rev 3822) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/actions/SimulationAction.java 2013-10-28 16:58:02 UTC (rev 3823) @@ -34,7 +34,7 @@ import org.apache.commons.io.FileUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.nuiton.util.ApplicationConfig.Action.Step; +import org.nuiton.config.ApplicationConfig.Action.Step; import org.nuiton.util.ZipUtil; import fr.ifremer.isisfish.IsisConfig; Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/types/hibernate/MatrixType.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/types/hibernate/MatrixType.java 2013-04-08 14:55:26 UTC (rev 3822) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/types/hibernate/MatrixType.java 2013-10-28 16:58:02 UTC (rev 3823) @@ -42,7 +42,7 @@ import org.nuiton.topia.persistence.TopiaEntity; import org.nuiton.util.StringUtil; import org.hibernate.HibernateException; -import org.hibernate.engine.SessionImplementor; +import org.hibernate.engine.spi.SessionImplementor; import org.hibernate.engine.jdbc.NonContextualLobCreator; import org.hibernate.type.StandardBasicTypes; import org.hibernate.type.Type; Modified: branches/4.0.1/src/test/java/fr/ifremer/isisfish/AbstractIsisFishTest.java =================================================================== --- branches/4.0.1/src/test/java/fr/ifremer/isisfish/AbstractIsisFishTest.java 2013-04-08 14:55:26 UTC (rev 3822) +++ branches/4.0.1/src/test/java/fr/ifremer/isisfish/AbstractIsisFishTest.java 2013-10-28 16:58:02 UTC (rev 3823) @@ -33,7 +33,7 @@ import org.junit.Before; import org.junit.BeforeClass; import org.nuiton.util.FileUtil; -import org.nuiton.util.config.ArgumentsParserException; +import org.nuiton.config.ArgumentsParserException; import fr.ifremer.isisfish.datastore.AutoMigrationIsisH2Config; import fr.ifremer.isisfish.datastore.CodeSourceStorage.Location;

1 0

Jenkins build became unstable: isis-fish #1988
by admin+hudson＠codelutin.com Sept. 12, 2013

Sept. 12, 2013

See <http://ci.nuiton.org/jenkins/job/isis-fish/1988/>

1 0

Build failed in Jenkins: isis-fish #1986
by admin+hudson＠codelutin.com Sept. 12, 2013

Sept. 12, 2013

See <http://ci.nuiton.org/jenkins/job/isis-fish/1986/> ------------------------------------------ Started by user Éric Chatellier Building on master in workspace <http://ci.nuiton.org/jenkins/job/isis-fish/ws/> Updating http://svn.forge.codelutin.com/svn/isis-fish/trunk at revision '2013-09-12T11:51:31.710 +0200' At revision 3822 no change for http://svn.forge.codelutin.com/svn/isis-fish/trunk since the previous build Parsing POMs Modules changed, recalculating dependency graph [trunk] $ /opt/jdk/bin/java -Xmx256m -XX:-UseGCOverheadLimit -Djava.awt.headless=true -cp /var/local/jenkins/data/plugins/maven-plugin/WEB-INF/lib/maven3-agent-1.3.jar:/opt/maven3/boot/plexus-classworlds-2.4.jar org.jvnet.hudson.maven3.agent.Maven3Main /opt/maven3 /opt/repository/apache-tomcat-7.0.42/webapps/jenkins/WEB-INF/lib/remoting-2.28.jar /var/local/jenkins/data/plugins/maven-plugin/WEB-INF/lib/maven3-interceptor-1.3.jar 39235 <===[JENKINS REMOTING CAPACITY]===> channel started log4j:WARN No appenders could be found for logger (org.apache.commons.beanutils.converters.BooleanConverter). log4j:WARN Please initialize the log4j system properly. Executing Maven: -B -f <http://ci.nuiton.org/jenkins/job/isis-fish/ws/trunk/pom.xml> -U -e clean install [INFO] Error stacktraces are turned on. [INFO] Scanning for projects... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building IsisFish 4.2.1.2-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: http://nexus.nuiton.org/nexus/content/groups/public/org/nuiton/jaxx/maven-j… Downloading: http://nexus.nuiton.org/nexus/content/groups/public/org/nuiton/jaxx/maven-j… [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.739s [INFO] Finished at: Thu Sep 12 11:51:36 CEST 2013 [INFO] Final Memory: 13M/240M [INFO] ------------------------------------------------------------------------ [JENKINS] Archiving <http://ci.nuiton.org/jenkins/job/isis-fish/ws/trunk/pom.xml> to /var/local/jenkins/data/jobs/isis-fish/modules/fr.ifremer$isis-fish/builds/2013-09-12_11-51-33/archive/fr.ifremer/isis-fish/4.2.1.2-SNAPSHOT/isis-fish-4.2.1.2-SNAPSHOT.pom Waiting for Jenkins to finish collecting data mavenExecutionResult exceptions not empty message : Plugin org.nuiton.jaxx:maven-jaxx-plugin:2.4.2 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.nuiton.jaxx:maven-jaxx-plugin:jar:2.4.2 cause : Failed to read artifact descriptor for org.nuiton.jaxx:maven-jaxx-plugin:jar:2.4.2 Stack trace : org.apache.maven.plugin.PluginResolutionException: Plugin org.nuiton.jaxx:maven-jaxx-plugin:2.4.2 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.nuiton.jaxx:maven-jaxx-plugin:jar:2.4.2 at org.apache.maven.plugin.internal.DefaultPluginDependenciesResolver.resolve(DefaultPluginDependenciesResolver.java:129) at org.apache.maven.plugin.internal.DefaultMavenPluginManager.getPluginDescriptor(DefaultMavenPluginManager.java:142) at org.apache.maven.plugin.internal.DefaultMavenPluginManager.getMojoDescriptor(DefaultMavenPluginManager.java:261) at org.apache.maven.plugin.DefaultBuildPluginManager.getMojoDescriptor(DefaultBuildPluginManager.java:185) at org.apache.maven.lifecycle.internal.DefaultLifecycleExecutionPlanCalculator.calculateLifecycleMappings(DefaultLifecycleExecutionPlanCalculator.java:280) at org.apache.maven.lifecycle.internal.DefaultLifecycleExecutionPlanCalculator.calculateMojoExecutions(DefaultLifecycleExecutionPlanCalculator.java:193) at org.apache.maven.lifecycle.internal.DefaultLifecycleExecutionPlanCalculator.calculateExecutionPlan(DefaultLifecycleExecutionPlanCalculator.java:112) at org.apache.maven.lifecycle.internal.DefaultLifecycleExecutionPlanCalculator.calculateExecutionPlan(DefaultLifecycleExecutionPlanCalculator.java:129) at org.apache.maven.lifecycle.internal.BuilderCommon.resolveBuildPlan(BuilderCommon.java:92) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:81) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59) at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183) at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161) at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:320) at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156) at org.jvnet.hudson.maven3.launcher.Maven3Launcher.main(Maven3Launcher.java:79) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.codehaus.plexus.classworlds.launcher.Launcher.launchStandard(Launcher.java:329) at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:239) at org.jvnet.hudson.maven3.agent.Maven3Main.launch(Maven3Main.java:174) at hudson.maven.Maven3Builder.call(Maven3Builder.java:100) at hudson.maven.Maven3Builder.call(Maven3Builder.java:66) at hudson.remoting.UserRequest.perform(UserRequest.java:118) at hudson.remoting.UserRequest.perform(UserRequest.java:48) at hudson.remoting.Request$2.run(Request.java:326) at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:72) at java.util.concurrent.FutureTask.run(FutureTask.java:262) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:724) Caused by: org.sonatype.aether.resolution.ArtifactDescriptorException: Failed to read artifact descriptor for org.nuiton.jaxx:maven-jaxx-plugin:jar:2.4.2 at org.apache.maven.repository.internal.DefaultArtifactDescriptorReader.loadPom(DefaultArtifactDescriptorReader.java:296) at org.apache.maven.repository.internal.DefaultArtifactDescriptorReader.readArtifactDescriptor(DefaultArtifactDescriptorReader.java:186) at org.sonatype.aether.impl.internal.DefaultRepositorySystem.readArtifactDescriptor(DefaultRepositorySystem.java:279) at org.apache.maven.plugin.internal.DefaultPluginDependenciesResolver.resolve(DefaultPluginDependenciesResolver.java:115) ... 32 more Caused by: org.sonatype.aether.resolution.ArtifactResolutionException: Could not transfer artifact org.nuiton.jaxx:maven-jaxx-plugin:pom:2.4.2 from/to nuiton.plugin.public (http://nexus.nuiton.org/nexus/content/groups/public) GET request of: org/nuiton/jaxx/maven-jaxx-plugin/2.4.2/maven-jaxx-plugin-2.4.2.pom from nuiton.plugin.public failed at org.sonatype.aether.impl.internal.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:538) at org.sonatype.aether.impl.internal.DefaultArtifactResolver.resolveArtifacts(DefaultArtifactResolver.java:216) at org.sonatype.aether.impl.internal.DefaultArtifactResolver.resolveArtifact(DefaultArtifactResolver.java:193) at org.apache.maven.repository.internal.DefaultArtifactDescriptorReader.loadPom(DefaultArtifactDescriptorReader.java:281) ... 35 more Caused by: org.sonatype.aether.transfer.ArtifactTransferException: Could not transfer artifact org.nuiton.jaxx:maven-jaxx-plugin:pom:2.4.2 from/to nuiton.plugin.public (http://nexus.nuiton.org/nexus/content/groups/public) GET request of: org/nuiton/jaxx/maven-jaxx-plugin/2.4.2/maven-jaxx-plugin-2.4.2.pom from nuiton.plugin.public failed at org.sonatype.aether.connector.wagon.WagonRepositoryConnector$4.wrap(WagonRepositoryConnector.java:951) at org.sonatype.aether.connector.wagon.WagonRepositoryConnector$4.wrap(WagonRepositoryConnector.java:941) at org.sonatype.aether.connector.wagon.WagonRepositoryConnector$GetTask.run(WagonRepositoryConnector.java:669) at org.sonatype.aether.util.concurrency.RunnableErrorForwarder$1.run(RunnableErrorForwarder.java:60) ... 3 more Caused by: org.apache.maven.wagon.TransferFailedException: GET request of: org/nuiton/jaxx/maven-jaxx-plugin/2.4.2/maven-jaxx-plugin-2.4.2.pom from nuiton.plugin.public failed at org.apache.maven.wagon.AbstractWagon.getTransfer(AbstractWagon.java:349) at org.apache.maven.wagon.AbstractWagon.getTransfer(AbstractWagon.java:310) at org.apache.maven.wagon.AbstractWagon.getTransfer(AbstractWagon.java:287) at org.apache.maven.wagon.StreamWagon.getIfNewer(StreamWagon.java:97) at org.apache.maven.wagon.StreamWagon.get(StreamWagon.java:61) at org.sonatype.aether.connector.wagon.WagonRepositoryConnector$GetTask.run(WagonRepositoryConnector.java:601) ... 4 more Caused by: java.io.FileNotFoundException: /var/local/maven/data/repository/org/nuiton/jaxx/maven-jaxx-plugin/2.4.2/maven-jaxx-plugin-2.4.2.pom.tmp0f04554893c2420a (Permission denied) at java.io.FileOutputStream.open(Native Method) at java.io.FileOutputStream.<init>(FileOutputStream.java:221) at java.io.FileOutputStream.<init>(FileOutputStream.java:171) at org.apache.maven.wagon.LazyFileOutputStream.initialize(LazyFileOutputStream.java:154) at org.apache.maven.wagon.LazyFileOutputStream.write(LazyFileOutputStream.java:126) at org.apache.maven.wagon.AbstractWagon.transfer(AbstractWagon.java:502) at org.apache.maven.wagon.AbstractWagon.getTransfer(AbstractWagon.java:339) ... 9 more Sending e-mails to: isis-fish-commits(a)list.isis-fish.org channel stopped

1 1

Build failed in Jenkins: isis-fish » IsisFish #1986
by admin+hudson＠codelutin.com Sept. 12, 2013

Sept. 12, 2013

See <http://ci.nuiton.org/jenkins/job/isis-fish/fr.ifremer$isis-fish/1986/> ------------------------------------------ <===[JENKINS REMOTING CAPACITY]===> channel started log4j:WARN No appenders could be found for logger (org.apache.commons.beanutils.converters.BooleanConverter). log4j:WARN Please initialize the log4j system properly. Executing Maven: -B -f <http://ci.nuiton.org/jenkins/job/isis-fish/fr.ifremer$isis-fish/ws/pom.xml> -U -e clean install [INFO] Error stacktraces are turned on. [INFO] Scanning for projects... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building IsisFish 4.2.1.2-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: http://nexus.nuiton.org/nexus/content/groups/public/org/nuiton/jaxx/maven-j… Downloading: http://nexus.nuiton.org/nexus/content/groups/public/org/nuiton/jaxx/maven-j…

1 1

r3822 - in branches/4.0.1: . src/main/java/fr/ifremer/isisfish src/main/java/fr/ifremer/isisfish/aspect src/main/java/fr/ifremer/isisfish/simulator/launcher src/main/java/fr/ifremer/isisfish/util src/main/resources
by echatellier＠users.forge.codelutin.com April 8, 2013

April 8, 2013

Author: echatellier Date: 2013-04-08 16:55:26 +0200 (Mon, 08 Apr 2013) New Revision: 3822 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3822 Log: fixes #2255 : Move from aspectwerkz to aspectj Added: branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/AspectJUrlClassLoader.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/AspectJWeavingAdaptor.java Removed: branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/AspectClassLoader.java Modified: branches/4.0.1/pom.xml branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisFish.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/CacheAspect.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/RuleAspect.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/TraceAspect.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/package-info.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/Cache.java branches/4.0.1/src/main/resources/log4j.properties Modified: branches/4.0.1/pom.xml =================================================================== --- branches/4.0.1/pom.xml 2013-03-11 17:04:52 UTC (rev 3821) +++ branches/4.0.1/pom.xml 2013-04-08 14:55:26 UTC (rev 3822) @@ -6,7 +6,7 @@ <parent> <groupId>org.nuiton</groupId> <artifactId>mavenpom4redmine</artifactId> - <version>3.4.8</version> + <version>3.4.9</version> </parent> <groupId>fr.ifremer</groupId> @@ -182,14 +182,14 @@ <dependency> <groupId>org.apache.commons</groupId> <artifactId>commons-math3</artifactId> - <version>3.1.1</version> + <version>3.2</version> <scope>runtime</scope>  </dependency> <dependency> <groupId>org.apache.commons</groupId> <artifactId>commons-email</artifactId> - <version>1.3</version> + <version>1.3.1</version> </dependency> <dependency> @@ -207,14 +207,14 @@ <dependency> <groupId>org.slf4j</groupId> <artifactId>slf4j-api</artifactId> - <version>1.7.2</version> + <version>1.7.5</version> <scope>runtime</scope> </dependency> <dependency> <groupId>org.slf4j</groupId> <artifactId>slf4j-log4j12</artifactId> - <version>1.7.2</version> + <version>1.7.5</version> <scope>runtime</scope> </dependency> @@ -288,7 +288,7 @@ <dependency> <groupId>com.h2database</groupId> <artifactId>h2</artifactId> - <version>1.3.170</version> + <version>1.3.171</version> <scope>compile</scope> </dependency> @@ -300,24 +300,20 @@ <scope>runtime</scope> </dependency> -  <dependency> - <groupId>aspectwerkz</groupId> - <artifactId>aspectwerkz</artifactId> - <version>${aspectwerkzVersion}</version> - <scope>compile</scope> + <groupId>org.aspectj</groupId> + <artifactId>aspectjrt</artifactId> + <version>1.7.2</version> </dependency> <dependency> - <groupId>aspectwerkz</groupId> - <artifactId>aspectwerkz-jdk5</artifactId> - <version>${aspectwerkzVersion}</version> - <scope>compile</scope> + <groupId>org.aspectj</groupId> + <artifactId>aspectjweaver</artifactId> + <version>1.7.2</version> </dependency> <dependency> - <groupId>aspectwerkz</groupId> - <artifactId>aspectwerkz-core</artifactId> - <version>${aspectwerkzVersion}</version> - <scope>compile</scope> + <groupId>org.aspectj</groupId> + <artifactId>aspectjtools</artifactId> + <version>1.7.2</version> </dependency>  @@ -484,17 +480,15 @@ <license.organizationName>Ifremer, Codelutin</license.organizationName> <maven.compiler.source>1.7</maven.compiler.source> <maven.compiler.target>1.7</maven.compiler.target> - <animal.sniffer.skip>true</animal.sniffer.skip>  - <jaxxVersion>2.5.12</jaxxVersion> - <eugeneVersion>2.6.1</eugeneVersion> - <topiaVersion>2.7.1</topiaVersion> - <hibernateVersion>3.6.10.Final</hibernateVersion> - <nuitonUtilsVersion>2.6.10</nuitonUtilsVersion> + <jaxxVersion>2.5.16</jaxxVersion> + <eugeneVersion>2.6.2</eugeneVersion> + <topiaVersion>2.8-SNAPSHOT</topiaVersion> + <hibernateVersion>4.2.0.Final</hibernateVersion> + <nuitonUtilsVersion>2.6.12</nuitonUtilsVersion> <nuitonI18nVersion>2.5</nuitonI18nVersion> <nuitonWidgetsVersion>1.1.1</nuitonWidgetsVersion> - <aspectwerkzVersion>2.0</aspectwerkzVersion> <redmine.releaseFiles>target/isis-fish-${project.version}-bin.zip</redmine.releaseFiles> Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisFish.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisFish.java 2013-03-11 17:04:52 UTC (rev 3821) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisFish.java 2013-04-08 14:55:26 UTC (rev 3822) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2005 - 2012 Ifremer, CodeLutin, Chatellier Eric + * Copyright (C) 2005 - 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 @@ -642,7 +642,7 @@ // using non recompiled script due to dependency changes // this is the better solution found : // remove isis build directory - FileUtils.deleteQuietly(IsisFish.config.getCompileDirectory()); + //FileUtils.deleteQuietly(IsisFish.config.getCompileDirectory()); ErrorHelper.showErrorDialog(null, _("isisfish.error.linkageerror.message"), cause); } Deleted: branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/AspectClassLoader.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/AspectClassLoader.java 2013-03-11 17:04:52 UTC (rev 3821) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/AspectClassLoader.java 2013-04-08 14:55:26 UTC (rev 3822) @@ -1,164 +0,0 @@ -/* - * #%L - * IsisFish - * - * $Id$ - * $HeadURL$ - * %% - * Copyright (C) 1999 - 2010 Ifremer, Code Lutin, Cédric Pineau, 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 - * 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.aspect; - -import java.io.IOException; -import java.net.URL; -import java.net.URLClassLoader; -import java.util.HashSet; -import java.util.Iterator; -import java.util.Set; - -import org.codehaus.aspectwerkz.annotation.AspectAnnotationParser; -import org.codehaus.aspectwerkz.definition.AdviceDefinition; -import org.codehaus.aspectwerkz.definition.AspectDefinition; -import org.codehaus.aspectwerkz.definition.DeploymentScope; -import org.codehaus.aspectwerkz.definition.SystemDefinition; -import org.codehaus.aspectwerkz.definition.SystemDefinitionContainer; -import org.codehaus.aspectwerkz.expression.ExpressionInfo; -import org.codehaus.aspectwerkz.hook.impl.ClassPreProcessorHelper; -import org.codehaus.aspectwerkz.reflect.ClassInfo; -import org.codehaus.aspectwerkz.reflect.impl.asm.AsmClassInfo; -import org.codehaus.aspectwerkz.reflect.impl.java.JavaClassInfo; -import org.codehaus.aspectwerkz.transform.inlining.AspectModelManager; - -import sun.misc.Resource; -import sun.misc.URLClassPath; - -/** - * Aspectwerkz class loader. - * - * http://aspectwerkz.codehaus.org/xref/org/codehaus/aspectwerkz/transform/inl… - * - * Created: 30 mars 07 00:31:22 - * - * @author poussin - * @version $Revision$ - * - * Last update: $Date$ - * by : $Author$ - */ -public class AspectClassLoader extends URLClassLoader { - - /** - * Class loader constructor. - * - * @param urls parent urlclassloader url - * @param parent parent class loader - */ - public AspectClassLoader(URL[] urls, ClassLoader parent) { - super(urls, parent); - ClassPreProcessorHelper.initializePreProcessor(); - } - - @Override - protected Class<?> findClass(String name) throws ClassNotFoundException { - String path = name.replace('.', '/').concat(".class"); - URLClassPath ucp = new URLClassPath(getURLs()); - Resource res = ucp.getResource(path, false); - if (res != null) { - //definePackage(name.substring(0, name.lastIndexOf(".")), null, null); - try { - byte[] b = res.getBytes(); - byte[] transformed = ClassPreProcessorHelper.defineClass0Pre(this, name, b, 0, b.length, null); - return defineClass(name, transformed, 0, transformed.length); - } catch (IOException e) { - throw new ClassNotFoundException("Can't build aspect for class", e); - } - } else { - throw new ClassNotFoundException(name); - } - } - - /** - * Register new aspect. - * - * @param aspectClass aspect class to register - */ - public void deploy(Class<?> aspectClass) { - String className = aspectClass.getName(); - try { - aspectClass = Class.forName(className, false, this); - } catch (ClassNotFoundException e) { - throw new RuntimeException("could not load class [" + className + "] in class loader [" + this + "]"); - } - - final ClassInfo aspectClassInfo = JavaClassInfo.getClassInfo(aspectClass); - - // create a new aspect def and fill it up with the annotation def from the aspect class - final SystemDefinition systemDef = SystemDefinitionContainer.getVirtualDefinitionAt(this); - final AspectDefinition newAspectDef = new AspectDefinition(className, aspectClassInfo, systemDef); - getNewExpressionsForAspect(aspectClass, newAspectDef, systemDef, DeploymentScope.MATCH_ALL); - } - - /** - * Returns a set with the new expressions for the advice in the aspect to deploy. - * - * @param aspectClass - * @param newAspectDef - * @param newAspectDef - * @param systemDef - * @param deploymentScope - * @return a set with the new expressions - */ - private Set getNewExpressionsForAspect(final Class aspectClass, - final AspectDefinition newAspectDef, - final SystemDefinition systemDef, - final DeploymentScope deploymentScope) { - final ClassLoader aspectLoader = aspectClass.getClassLoader(); - final String aspectName = aspectClass.getName(); - - final ClassInfo classInfo = AsmClassInfo.getClassInfo(aspectName, aspectLoader); - - AspectModelManager.defineAspect(classInfo, newAspectDef, aspectLoader); - - AspectAnnotationParser.parse(classInfo, newAspectDef, aspectLoader); - - AspectDefinition aspectDef = systemDef.getAspectDefinition(aspectName); - if (aspectDef != null) { - // if in def already reuse some of the settings that can have been overridded by XML def - newAspectDef.setContainerClassName(aspectDef.getContainerClassName()); - newAspectDef.setDeploymentModel(aspectDef.getDeploymentModel()); - } - - systemDef.addAspectOverwriteIfExists(newAspectDef); - - final Set newExpressions = new HashSet(); - for (Iterator it2 = newAspectDef.getAdviceDefinitions().iterator(); it2.hasNext();) { - AdviceDefinition adviceDef = (AdviceDefinition) it2.next(); - ExpressionInfo oldExpression = adviceDef.getExpressionInfo(); - if (oldExpression == null) { - continue; - } - // deploymentHandle.registerDefinitionChange(adviceDef, oldExpression); - - final ExpressionInfo newExpression = deploymentScope.newExpressionInfo(oldExpression); - adviceDef.setExpressionInfo(newExpression); - newExpressions.add(newExpression); - } - return newExpressions; - } -} Added: branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/AspectJUrlClassLoader.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/AspectJUrlClassLoader.java (rev 0) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/AspectJUrlClassLoader.java 2013-04-08 14:55:26 UTC (rev 3822) @@ -0,0 +1,156 @@ +/* + * #%L + * IsisFish + * + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2013 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.aspect; + +import java.io.IOException; +import java.net.URL; +import java.security.CodeSource; +import java.util.HashMap; +import java.util.Map; + +import org.aspectj.bridge.AbortException; +import org.aspectj.weaver.bcel.ExtensibleURLClassLoader; +import org.aspectj.weaver.tools.Trace; +import org.aspectj.weaver.tools.TraceFactory; +import org.aspectj.weaver.tools.WeavingClassLoader; + +public class AspectJUrlClassLoader extends ExtensibleURLClassLoader implements WeavingClassLoader { + + public static final String WEAVING_CLASS_PATH = "aj.class.path"; + public static final String WEAVING_ASPECT_PATH = "aj.aspect.path"; + + private URL[] aspectURLs; + private AspectJWeavingAdaptor adaptor; + private boolean initializingAdaptor; + private Map generatedClasses = new HashMap(); /* String -> byte[] */ + + private static Trace trace = TraceFactory.getTraceFactory().getTrace(AspectJUrlClassLoader.class); + + public AspectJUrlClassLoader(URL[] urls, ClassLoader parent) { + super(urls, parent); + if (trace.isTraceEnabled()) + trace.enter("<init>", this, new Object[] { urls, parent }); + if (trace.isTraceEnabled()) + trace.exit("<init>"); + + adaptor = new AspectJWeavingAdaptor(getParent(), this); + } + + private static String getAspectPath() { + return System.getProperty(WEAVING_ASPECT_PATH, ""); + } + + private static String getClassPath() { + return System.getProperty(WEAVING_CLASS_PATH, ""); + } + + protected void addURL(URL url) { + adaptor.addURL(url); + super.addURL(url); + } + + /** + * Override to weave class using WeavingAdaptor + */ + protected Class defineClass(String name, byte[] b, CodeSource cs) throws IOException { + if (trace.isTraceEnabled()) + trace.enter("defineClass", this, new Object[] { name, b, cs }); + // System.err.println("? WeavingURLClassLoader.defineClass(" + name + ", [" + b.length + "])"); + byte orig[] = b; + /* Avoid recursion during adaptor initialization */ + if (!initializingAdaptor) { + + /* Need to defer creation because of possible recursion during constructor execution */ + if (adaptor == null && !initializingAdaptor) { + //createAdaptor(); + } + + try { + b = adaptor.weaveClass(name, b, false); + } catch (AbortException ex) { + trace.error("defineClass", ex); + throw ex; + } catch (Throwable th) { + trace.error("defineClass", th); + } + } + Class clazz; + + // On error, define the original form of the class and log the issue + try { + clazz= super.defineClass(name, b, cs); + } catch (Throwable th) { + trace.error("Weaving class problem. Original class has been returned. The error was caused because of: " + th, th); + clazz= super.defineClass(name, orig, cs); + } + if (trace.isTraceEnabled()) + trace.exit("defineClass", clazz); + return clazz; + } + + /** + * Override to find classes generated by WeavingAdaptor + */ + protected byte[] getBytes(String name) throws IOException { + byte[] bytes = super.getBytes(name); + + if (bytes == null) { + // return adaptor.findClass(name); + return (byte[]) generatedClasses.remove(name); + } + + return bytes; + } + + /** + * Implement method from WeavingClassLoader + */ + public URL[] getAspectURLs() { + return aspectURLs; + } + + public void acceptClass (String name, byte[] classBytes, byte[] weavedBytes) { + generatedClasses.put(name, weavedBytes); + } + + public void deploy(Class<?> aspectClass) { + byte[] result = adaptor.deploy(aspectClass); + // this classloader need to be implemented in "local first" strategy + // and aspectized class must be forced into current classloader + // otherwize, aspectj will complain about missing 'aspectOf' methods + defineClass(aspectClass.getName(), result, 0, result.length); + } + + /** + * Mark classloader as configured with aspects and tell to prepare for + * weaving. + * + * Must call this method to avoid NPE in aspectj weaver. + */ + public void prepare() { + adaptor.prepare(); + } +} Property changes on: branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/AspectJUrlClassLoader.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/AspectJWeavingAdaptor.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/AspectJWeavingAdaptor.java (rev 0) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/AspectJWeavingAdaptor.java 2013-04-08 14:55:26 UTC (rev 3822) @@ -0,0 +1,237 @@ +/* + * #%L + * IsisFish + * + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2013 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.aspect; + +import java.io.ByteArrayInputStream; +import java.io.IOException; +import java.io.InputStream; +import java.lang.reflect.Field; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; + +import org.aspectj.apache.bcel.classfile.ClassParser; +import org.aspectj.apache.bcel.classfile.JavaClass; +import org.aspectj.bridge.IMessageHandler; +import org.aspectj.util.FileUtil; +import org.aspectj.util.LangUtil; +import org.aspectj.weaver.CrosscuttingMembersSet; +import org.aspectj.weaver.IClassFileProvider; +import org.aspectj.weaver.IUnwovenClassFile; +import org.aspectj.weaver.IWeaveRequestor; +import org.aspectj.weaver.ResolvedType; +import org.aspectj.weaver.bcel.BcelObjectType; +import org.aspectj.weaver.bcel.BcelWeaver; +import org.aspectj.weaver.bcel.BcelWorld; +import org.aspectj.weaver.bcel.UnwovenClassFile; +import org.aspectj.weaver.tools.WeavingAdaptor; +import org.aspectj.weaver.tools.WeavingClassLoader; +import org.aspectj.weaver.tools.cache.SimpleCache; +import org.aspectj.weaver.tools.cache.SimpleCacheFactory; + +public class AspectJWeavingAdaptor extends WeavingAdaptor { + + protected ClassLoader parentLoader; + + protected CrosscuttingMembersSet xcutSet; + + public AspectJWeavingAdaptor(ClassLoader parentLoader, WeavingClassLoader loader) { + this.parentLoader = parentLoader; + + generatedClassHandler = loader; + init((ClassLoader)loader, getFullClassPath((ClassLoader) loader)); + } + + /** + * Initialize the WeavingAdapter + * @param loader ClassLoader used by this adapter; which can be null + * @param classPath classpath of this adapter + * @param aspectPath list of aspect paths + */ + private void init(ClassLoader loader, List<String> classPath) { + try { + //XXX call to private code "abortOnError = true;" + Field abortOnErrorField = WeavingAdaptor.class.getDeclaredField("abortOnError"); + abortOnErrorField.setAccessible(true); + abortOnErrorField.set(this, true); + + createMessageHandler(); + + info("using classpath: " + classPath); + //info("using aspectpath: " + aspectPath); + + Field messageHandlerField = WeavingAdaptor.class.getDeclaredField("messageHandler"); + messageHandlerField.setAccessible(true); + IMessageHandler messageHandler = (IMessageHandler)messageHandlerField.get(this); + bcelWorld = new BcelWorld(classPath, messageHandler, null); + bcelWorld.setXnoInline(false); + bcelWorld.getLint().loadDefaultProperties(); + if (LangUtil.is15VMOrGreater()) { + bcelWorld.setBehaveInJava5Way(true); + } + + weaver = new BcelWeaver(bcelWorld); + //registerAspectLibraries(aspectPath); + //initializeCache(loader, aspectPath, null, getMessageHandler()); + + //XXX call to private code "enabled = true;" + Field enabledField = WeavingAdaptor.class.getDeclaredField("enabled"); + enabledField.setAccessible(true); + enabledField.set(this, true); + + // get private field instance + //XXX call to private code "xcutSet = weaver.xcutSet" + Field xcutSetField = BcelWeaver.class.getDeclaredField("xcutSet"); + xcutSetField.setAccessible(true); + xcutSet = (CrosscuttingMembersSet) xcutSetField.get(weaver); + + } catch (NoSuchFieldException | SecurityException | IllegalArgumentException | IllegalAccessException e) { + e.printStackTrace(); + } + } + + public byte[] deploy(Class<?> aspectClass) { + byte[] result = null; + try { + String name = aspectClass.getName(); + InputStream is = AspectJWeavingAdaptor.class.getResourceAsStream("/" + name.replace('.', '/') + ".class"); + byte[] bytes = FileUtil.readAsByteArray(is); + is.close(); + ClassParser parser = new ClassParser(new ByteArrayInputStream(bytes), name); + + JavaClass jc = parser.parse(); + BcelObjectType bcType = bcelWorld.addSourceObjectType(jc, false); + ResolvedType type = bcType.getResolvedTypeX(); + xcutSet.addOrReplaceAspect(type); + + WeavingClassFileProvider2 wcp = new WeavingClassFileProvider2(name, bytes); + wcp.setApplyAtAspectJMungersOnly(); + weaver.weave(wcp); + result = wcp.getBytes(); + + } catch (IOException e) { + throw new RuntimeException("Can't create aspect", e); + } + + return result; + } + + /** + * Mark bcel weaver ready for weaving classes. + */ + public void prepare() { + weaver.prepareForWeave(); + } + + private class WeavingClassFileProvider2 implements IClassFileProvider { + + private final UnwovenClassFile unwovenClass; + private final List<UnwovenClassFile> unwovenClasses = new ArrayList<UnwovenClassFile>(); + private IUnwovenClassFile wovenClass; + private boolean isApplyAtAspectJMungersOnly = false; + + public WeavingClassFileProvider2(String name, byte[] bytes) { + ensureDelegateInitialized(name, bytes); + this.unwovenClass = new UnwovenClassFile(name, name /*delegateForCurrentClass.getResolvedTypeX().getName()*/, bytes); + this.unwovenClasses.add(unwovenClass); + + if (shouldDump(name.replace('/', '.'), true)) { + dump(name, bytes, true); + } + + } + + public void setApplyAtAspectJMungersOnly() { + isApplyAtAspectJMungersOnly = true; + } + + public boolean isApplyAtAspectJMungersOnly() { + return isApplyAtAspectJMungersOnly; + } + + public byte[] getBytes() { + if (wovenClass != null) { + return wovenClass.getBytes(); + } else { + return unwovenClass.getBytes(); + } + } + + public Iterator<UnwovenClassFile> getClassFileIterator() { + return unwovenClasses.iterator(); + } + + public IWeaveRequestor getRequestor() { + return new IWeaveRequestor() { + + public void acceptResult(IUnwovenClassFile result) { + if (wovenClass == null) { + wovenClass = result; + String name = result.getClassName(); + if (shouldDump(name.replace('/', '.'), false)) { + dump(name, result.getBytes(), false); + } + } else { + // Classes generated by weaver e.g. around closure advice + String className = result.getClassName(); + byte[] resultBytes = result.getBytes(); + + if (SimpleCacheFactory.isEnabled()) { + SimpleCache lacache=SimpleCacheFactory.createSimpleCache(); + lacache.put(result.getClassName(), wovenClass.getBytes(), result.getBytes()); + lacache.addGeneratedClassesNames(wovenClass.getClassName(), wovenClass.getBytes(), result.getClassName()); + } + + generatedClasses.put(className, result); + generatedClasses.put(wovenClass.getClassName(), result); + generatedClassHandler.acceptClass(className, null, resultBytes); + } + } + + public void processingReweavableState() { + } + + public void addingTypeMungers() { + } + + public void weavingAspects() { + } + + public void weavingClasses() { + } + + public void weaveCompleted() { + // ResolvedType.resetPrimitives(); + if (delegateForCurrentClass != null) { + delegateForCurrentClass.weavingCompleted(); + } + // ResolvedType.resetPrimitives(); + // bcelWorld.discardType(typeBeingProcessed.getResolvedTypeX()); // work in progress + } + }; + } + } +} Property changes on: branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/AspectJWeavingAdaptor.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/CacheAspect.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/CacheAspect.java 2013-03-11 17:04:52 UTC (rev 3821) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/CacheAspect.java 2013-04-08 14:55:26 UTC (rev 3822) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2006 - 2010 Ifremer, Code Lutin, Cédric Pineau, Benjamin Poussin + * Copyright (C) 2006 - 2013 Ifremer, Code Lutin, Cédric Pineau, 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 @@ -30,13 +30,10 @@ import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.codehaus.aspectwerkz.annotation.Around; -import org.codehaus.aspectwerkz.annotation.Aspect; -import org.codehaus.aspectwerkz.annotation.Expression; -import org.codehaus.aspectwerkz.definition.Pointcut; -import org.codehaus.aspectwerkz.joinpoint.JoinPoint; -import org.codehaus.aspectwerkz.joinpoint.MethodRtti; -import org.codehaus.aspectwerkz.joinpoint.MethodSignature; +import org.aspectj.lang.ProceedingJoinPoint; +import org.aspectj.lang.annotation.Around; +import org.aspectj.lang.annotation.Aspect; +import org.aspectj.lang.reflect.MethodSignature; import fr.ifremer.isisfish.simulator.SimulationContext; import fr.ifremer.isisfish.util.Cache; @@ -52,14 +49,14 @@ * Last update: $Date$ * by : $Author$ */ -@Aspect("perJVM") +@Aspect public class CacheAspect { /** to use log facility, just put in your code: log.info(\"...\"); */ static private Log log = LogFactory.getLog(CacheAspect.class); - @Expression("execution(* scripts..*(..))") - Pointcut scriptsMethod; + //@Expression("execution(* scripts..*(..))") + //Pointcut scriptsMethod; public CacheAspect() { } @@ -74,16 +71,16 @@ Cache result = context.getCache(); return result; } - - @Around("scriptsMethod") - public Object call(final JoinPoint jp) throws Throwable { + + @Around("execution(* scripts..*(..))") + public Object call(final ProceedingJoinPoint jp) throws Throwable { Method method = ((MethodSignature)jp.getSignature()).getMethod(); - Object[] args = ((MethodRtti)jp.getRtti()).getParameterValues(); + Object[] args = jp.getArgs(); Object result = getCache().get(method, args, jp); if (log.isTraceEnabled()) { log.trace(((MethodSignature)jp.getSignature()).getMethod() - + " args " + Arrays.toString(((MethodRtti)jp.getRtti()).getParameterValues()) + + " args " + Arrays.toString(jp.getArgs()) + " result = " + result); } return result; Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/RuleAspect.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/RuleAspect.java 2013-03-11 17:04:52 UTC (rev 3821) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/RuleAspect.java 2013-04-08 14:55:26 UTC (rev 3822) @@ -27,9 +27,10 @@ import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.codehaus.aspectwerkz.annotation.Around; -import org.codehaus.aspectwerkz.annotation.Aspect; -import org.codehaus.aspectwerkz.joinpoint.JoinPoint; +import org.aspectj.lang.JoinPoint; +import org.aspectj.lang.ProceedingJoinPoint; +import org.aspectj.lang.annotation.Around; +import org.aspectj.lang.annotation.Aspect; import fr.ifremer.isisfish.datastore.SimulationInformation; import fr.ifremer.isisfish.datastore.SimulationStorage; @@ -50,7 +51,7 @@ * Last update : $Date$ * By : $Author$ */ -@Aspect("perInstance") +@Aspect public class RuleAspect { /** @@ -71,7 +72,7 @@ * @throws Throwable */ @Around("execution(* rules.*.init(..))") - public Object initCall(final JoinPoint jp) throws Throwable { + public Object initCall(final ProceedingJoinPoint jp) throws Throwable { Object result = makeTimedCall(jp, State.INIT); return result; @@ -86,7 +87,7 @@ * @throws Throwable */ @Around("execution(* rules.*.preAction(..))") - public Object initPreCall(final JoinPoint jp) throws Throwable { + public Object initPreCall(final ProceedingJoinPoint jp) throws Throwable { Object result = makeTimedCall(jp, State.PRE); return result; @@ -100,7 +101,7 @@ * @throws Throwable */ @Around("execution(* rules.*.postAction(..))") - public Object initPostCall(final JoinPoint jp) throws Throwable { + public Object initPostCall(final ProceedingJoinPoint jp) throws Throwable { Object result = makeTimedCall(jp, State.POST); return result; @@ -113,10 +114,10 @@ * @param state state * @throws Throwable */ - protected Object makeTimedCall(JoinPoint jp, State state) throws Throwable { + protected Object makeTimedCall(ProceedingJoinPoint jp, State state) throws Throwable { if (log.isTraceEnabled()) { - log.trace("Rule aspect called : " + jp.getCalleeClass().getSimpleName()); + log.trace("Rule aspect called : " + jp.getTarget().getClass().getSimpleName()); } // get time before @@ -155,7 +156,7 @@ if (simulation != null) { // get rule information - Class<?> calleeClass = jp.getCalleeClass(); + Class<?> calleeClass = jp.getTarget().getClass(); String ruleName = calleeClass.getSimpleName(); SimulationInformation info = simulation.getInformation(); Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/TraceAspect.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/TraceAspect.java 2013-03-11 17:04:52 UTC (rev 3821) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/TraceAspect.java 2013-04-08 14:55:26 UTC (rev 3822) @@ -27,14 +27,12 @@ import java.lang.reflect.Method; -import org.codehaus.aspectwerkz.annotation.After; -import org.codehaus.aspectwerkz.annotation.AfterThrowing; -import org.codehaus.aspectwerkz.annotation.Aspect; -import org.codehaus.aspectwerkz.annotation.Before; -import org.codehaus.aspectwerkz.annotation.Expression; -import org.codehaus.aspectwerkz.definition.Pointcut; -import org.codehaus.aspectwerkz.joinpoint.JoinPoint; -import org.codehaus.aspectwerkz.joinpoint.MethodSignature; +import org.aspectj.lang.JoinPoint; +import org.aspectj.lang.annotation.After; +import org.aspectj.lang.annotation.AfterThrowing; +import org.aspectj.lang.annotation.Aspect; +import org.aspectj.lang.annotation.Before; +import org.aspectj.lang.reflect.MethodSignature; import fr.ifremer.isisfish.simulator.SimulationContext; import fr.ifremer.isisfish.util.Trace; @@ -53,15 +51,15 @@ * Last update: $Date$ * by : $Author$ */ -@Aspect("perJVM") +@Aspect public class TraceAspect { - @Expression("execution(* scripts..*(..))" + /*@Pointcut("execution(* scripts..*(..))" + " || execution(* simulators..*(..))" + " || execution(* rules..*(..)) " + " || execution(* simulationplans..*(..)) " + " || execution(* formules..*(..))") - Pointcut executeMethod; + Pointcut executeMethod;*/ public TraceAspect() { } @@ -77,18 +75,31 @@ return result; } - @Before("executeMethod") + @Before("execution(* scripts..*(..))" + + " || execution(* simulators..*(..))" + + " || execution(* rules..*(..)) " + + " || execution(* simulationplans..*(..)) " + + " || execution(* formules..*(..))") public void traceBeforeExecute(JoinPoint jp) { getTrace().traceBefore(); } - @AfterThrowing(type = "java.lang.Exception", pointcut = "executeMethod") - public void traceAfterThrowingExecute(JoinPoint jp) { + @AfterThrowing(throwing = "ex", + pointcut = "execution(* scripts..*(..))" + + " || execution(* simulators..*(..))" + + " || execution(* rules..*(..)) " + + " || execution(* simulationplans..*(..)) " + + " || execution(* formules..*(..))") + public void traceAfterThrowingExecute(JoinPoint jp, Exception ex) { // si une exeption est leve, il faut faire la meme chose traceAfterExecute(jp); } - @After("executeMethod") + @After("execution(* scripts..*(..))" + + " || execution(* simulators..*(..))" + + " || execution(* rules..*(..)) " + + " || execution(* simulationplans..*(..)) " + + " || execution(* formules..*(..))") public void traceAfterExecute(JoinPoint jp) { Method method = ((MethodSignature) jp.getSignature()).getMethod(); getTrace().traceAfterCall(method); Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/package-info.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/package-info.java 2013-03-11 17:04:52 UTC (rev 3821) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/package-info.java 2013-04-08 14:55:26 UTC (rev 3822) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 1999 - 2010 Ifremer, CodeLutin + * Copyright (C) 1999 - 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 @@ -27,8 +27,8 @@ * * Contains two aspects : * <ul> - * <li>{@link fr.ifremer.isisfish.aspect.Cache} : cache aspect</li> - * <li>{@link fr.ifremer.isisfish.aspect.Trace} : trace expect</li> + * <li>{@link fr.ifremer.isisfish.aspect.CacheAspect} : cache aspect</li> + * <li>{@link fr.ifremer.isisfish.aspect.TraceAspect} : trace expect</li> * <li>{@link fr.ifremer.isisfish.aspect.RuleAspect} : rule timing aspect</li> * </ul> */ Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2013-03-11 17:04:52 UTC (rev 3821) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2013-04-08 14:55:26 UTC (rev 3822) @@ -37,6 +37,7 @@ import java.util.List; import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.time.DurationFormatUtils; import org.apache.commons.logging.Log; @@ -52,7 +53,7 @@ import fr.ifremer.isisfish.IsisConfig; import fr.ifremer.isisfish.IsisFish; import fr.ifremer.isisfish.IsisFishRuntimeException; -import fr.ifremer.isisfish.aspect.AspectClassLoader; +import fr.ifremer.isisfish.aspect.AspectJUrlClassLoader; import fr.ifremer.isisfish.aspect.CacheAspect; import fr.ifremer.isisfish.aspect.RuleAspect; import fr.ifremer.isisfish.aspect.TraceAspect; @@ -276,17 +277,14 @@ * @param directory le répertoire qui servira pour le classloader * @return le classe loader modifié */ - protected AspectClassLoader changeClassLoader(Thread thread, File directory) { + protected AspectJUrlClassLoader changeClassLoader(Thread thread, File directory) { try { URL[] classpath = new URL[] { directory.toURI().toURL(), // poussin 20080821 : il semble ne plus trouve les formules, // est-ce mieux avec le compile dir ? IsisFish.config.getCompileDirectory().toURI().toURL() }; - //URL [] classpath = new URL[]{directory.toURL()}; - AspectClassLoader loader = new AspectClassLoader(classpath, - IsisFish.class.getClassLoader()); //new URLClassLoader(classpath); - //AspectClassLoader loader = new AspectClassLoader(classpath, ClassLoader.getSystemClassLoader()); - //new URLClassLoader(classpath); + AspectJUrlClassLoader loader = new AspectJUrlClassLoader(classpath, + IsisFish.class.getClassLoader()); thread.setContextClassLoader(loader); log.info("Classloader used for simulation: " + loader + " " + Arrays.toString(loader.getURLs())); @@ -318,7 +316,7 @@ + IsisConfig.getVersion()); long start = System.nanoTime(); simulation.getInformation().setSimulationStart(new java.util.Date()); - AspectClassLoader classLoader; + AspectJUrlClassLoader classLoader = null; try { File rootDirectory = simulation.getDirectory(); @@ -364,6 +362,8 @@ } } + classLoader.prepare(); + // recherche du simulateur a utiliser String simulatorName = parameters.getSimulatorName(); SimulatorStorage simulator = SimulatorStorage @@ -474,6 +474,12 @@ simulation.getInformation().setOptimizationUsage(cache); } + // try to fix memory leak + LogFactory.release(classLoader); + + // close classloader to release resource + IOUtils.closeQuietly(classLoader); + // cleanup specific context build directory File simulationBuildDirectory = IsisFish.config.getCompileDirectory(); if (log.isDebugEnabled()) { Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/Cache.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/Cache.java 2013-03-11 17:04:52 UTC (rev 3821) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/Cache.java 2013-04-08 14:55:26 UTC (rev 3822) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2006 - 2010 Ifremer, Code Lutin, Cédric Pineau, Benjamin Poussin + * Copyright (C) 2006 - 2013 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 @@ -29,7 +29,7 @@ import java.util.Map; import org.apache.commons.collections.map.ReferenceMap; -import org.codehaus.aspectwerkz.joinpoint.JoinPoint; +import org.aspectj.lang.ProceedingJoinPoint; import org.nuiton.topia.persistence.TopiaEntity; import fr.ifremer.isisfish.simulator.SimulationContext; @@ -196,8 +196,8 @@ */ protected Object realCall(Object defaultValue) throws Throwable { Object result = defaultValue; - if (defaultValue instanceof JoinPoint) { - result = ((JoinPoint)defaultValue).proceed(); + if (defaultValue instanceof ProceedingJoinPoint) { + result = ((ProceedingJoinPoint)defaultValue).proceed(); } return result; } Modified: branches/4.0.1/src/main/resources/log4j.properties =================================================================== --- branches/4.0.1/src/main/resources/log4j.properties 2013-03-11 17:04:52 UTC (rev 3821) +++ branches/4.0.1/src/main/resources/log4j.properties 2013-04-08 14:55:26 UTC (rev 3822) @@ -5,7 +5,7 @@ # $Id$ # $HeadURL$ # %% -# Copyright (C) 2005 - 2011 Ifremer, CodeLutin, Chatellier Eric +# Copyright (C) 2005 - 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

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