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

r3669 - trunk/src/main/resources/templates/ssh
by echatellier＠users.forge.codelutin.com March 30, 2012

March 30, 2012

Author: echatellier Date: 2012-03-30 15:32:08 +0200 (Fri, 30 Mar 2012) New Revision: 3669 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3669 Log: Configuration de R sur caparmor Modified: trunk/src/main/resources/templates/ssh/qsub-script.ftl Modified: trunk/src/main/resources/templates/ssh/qsub-script.ftl =================================================================== --- trunk/src/main/resources/templates/ssh/qsub-script.ftl 2012-03-30 13:18:49 UTC (rev 3668) +++ trunk/src/main/resources/templates/ssh/qsub-script.ftl 2012-03-30 13:32:08 UTC (rev 3669) @@ -5,7 +5,7 @@ $Id$ $HeadURL$ %% - Copyright (C) 2009 - 2011 Ifremer, CodeLutin, Chatellier Eric + Copyright (C) 2009 - 2012 Ifremer, CodeLutin, Chatellier Eric %% This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as @@ -26,10 +26,10 @@ cd "${isishome}" -#source /usr/share/modules/init/csh -#module load java/1.6.0 +module load R/2.14.2-gnu-4.3 -<#assign commonCommand="${javapath} -Xmx2000M -jar isis-fish*.jar --option launch.ui false --option perform.vcsupdate false --option perform.migration false --option perform.cron false" /> +<#assign commonCommand="${javapath} -Djava.library.path=jri64 -DR.type=jni -Xmx2000M -jar isis-fish*.jar" /> +<#assign commonOptions="--option launch.ui false --option perform.vcsupdate false --option perform.migration false --option perform.cron false" /> <#if qsubmutiplejob> <#-- localsimulationid is short simulation id version --> <#assign localsimulationid='${simulationid}_$PBS_ARRAY_INDEX' /> @@ -49,9 +49,9 @@ <#assign localsimulationoutput='${isistemp}simulation-${simulationid}-output.txt' /> </#if> <#if simulationprescript?length > 0> -${commonCommand} --simulateRemotellyWithPreScript "${localsimulationid}" "${localsimulationzip}" "${localsimulationresultzip}" "${localsimulationprescript}" >& "${localsimulationoutput}" +${commonCommand} ${commonOptions} --simulateRemotellyWithPreScript "${localsimulationid}" "${localsimulationzip}" "${localsimulationresultzip}" "${localsimulationprescript}" >& "${localsimulationoutput}" <#else> -${commonCommand} --simulateRemotelly "${localsimulationid}" "${localsimulationzip}" "${localsimulationresultzip}" >& "${localsimulationoutput}" +${commonCommand} ${commonOptions} --simulateRemotelly "${localsimulationid}" "${localsimulationzip}" "${localsimulationresultzip}" >& "${localsimulationoutput}" </#if> -rm -rf "$HOME/isis-database-3/simulations/${localsimulationid}" +rm -rf "$HOME/isis-fish-4/isis-database/simulations/${localsimulationid}"

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r3668 - trunk/src/main/java/fr/ifremer/isisfish/datastore
by echatellier＠users.forge.codelutin.com March 30, 2012

March 30, 2012

Author: echatellier Date: 2012-03-30 15:18:49 +0200 (Fri, 30 Mar 2012) New Revision: 3668 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3668 Log: Fix official/comm database location : simulation database was not used anymore (context) Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/CodeSourceStorage.java Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/CodeSourceStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/CodeSourceStorage.java 2012-03-20 09:52:07 UTC (rev 3667) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/CodeSourceStorage.java 2012-03-30 13:18:49 UTC (rev 3668) @@ -61,12 +61,17 @@ * Location enum to look for script in official repository or * community directory. * + * Il y a un gros méchant hack qui tache car on ne peut pas initialiser + * un repertoire en particulier pour OFFICIAL. Certaines fois, cela + * depend du context de simulation, donc on ne la définie que lors de + * l'appel a getDirectories(). + * * Implements iterable to be used in JavaFileManager. */ - public static enum Location implements Iterable<File> { + public static enum Location { OFFICIAL(IsisFish.config.getDatabaseDirectory()), COMMUNITY(IsisFish.config.getCommunityDatabaseDirectory()), - ALL(IsisFish.config.getDatabaseDirectory(), IsisFish.config.getCommunityDatabaseDirectory()); + ALL(null, IsisFish.config.getCommunityDatabaseDirectory()); protected File[] directory; private Location(File... directory) { @@ -74,21 +79,20 @@ } public File[] getDirectories() { - return directory; + File[] result = new File[this.directory.length]; + for (int i = 0 ; i < result.length ; i++) { + if (directory[i] == null) { + result[i] = IsisFish.config.getContextDatabaseDirectory(); + } else { + result[i] = directory[i]; + } + } + return result; } public void setDirectory(File... directory) { this.directory = directory; } - - /* - * @see java.lang.Iterable#iterator() - */ - @Override - public Iterator<File> iterator() { - List<File> files = Arrays.asList(directory); - return files.iterator(); - } } /**

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r3667 - branches/4.1
by echatellier＠users.forge.codelutin.com March 20, 2012

March 20, 2012

Author: echatellier Date: 2012-03-20 10:52:07 +0100 (Tue, 20 Mar 2012) New Revision: 3667 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3667 Log: #822: Update to nuiton-utils 2.4.5 #823: Update to topia 2.6.8 Modified: branches/4.1/pom.xml Modified: branches/4.1/pom.xml =================================================================== --- branches/4.1/pom.xml 2012-03-20 09:45:00 UTC (rev 3666) +++ branches/4.1/pom.xml 2012-03-20 09:52:07 UTC (rev 3667) @@ -538,9 +538,9 @@  <jaxxVersion>2.4.2</jaxxVersion> <eugeneVersion>2.4.2</eugeneVersion> - <topiaVersion>2.6.6</topiaVersion> + <topiaVersion>2.6.8</topiaVersion> <hibernateVersion>3.6.10.Final</hibernateVersion> - <nuitonUtilsVersion>2.4.4</nuitonUtilsVersion> + <nuitonUtilsVersion>2.4.5</nuitonUtilsVersion> <nuitonI18nVersion>2.4.1</nuitonI18nVersion> <nuitonWidgetsVersion>1.1.1</nuitonWidgetsVersion> <aspectwerkzVersion>2.0</aspectwerkzVersion>

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r3666 - branches/4.1
by echatellier＠users.forge.codelutin.com March 20, 2012

March 20, 2012

Author: echatellier Date: 2012-03-20 10:45:00 +0100 (Tue, 20 Mar 2012) New Revision: 3666 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3666 Log: Update to h2 1.3.165 Modified: branches/4.1/pom.xml Modified: branches/4.1/pom.xml =================================================================== --- branches/4.1/pom.xml 2012-03-20 08:59:58 UTC (rev 3665) +++ branches/4.1/pom.xml 2012-03-20 09:45:00 UTC (rev 3666) @@ -292,7 +292,7 @@ <dependency> <groupId>com.h2database</groupId> <artifactId>h2</artifactId> - <version>1.3.164</version> + <version>1.3.165</version> <scope>compile</scope> </dependency>

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r3665 - in branches: . 4.0.0-svnkit
by echatellier＠users.forge.codelutin.com March 20, 2012

March 20, 2012

Author: echatellier Date: 2012-03-20 09:59:58 +0100 (Tue, 20 Mar 2012) New Revision: 3665 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3665 Log: New branche for svnkit test Added: branches/4.0.0-svnkit/ Property changes on: branches/4.0.0-svnkit ___________________________________________________________________ Added: svn:ignore + maven.log target velocity.log .classpath .project isis-fish.ipr isis-fish.iws isis-fish.iml .settings bin nbproject Inputs_Langoustine Added: svn:mergeinfo +

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r3664 - in branches/4.0.1/src: main/java/fr/ifremer/isisfish/mexico/xml test/java/fr/ifremer/isisfish/mexico test/resources/mexico
by echatellier＠users.forge.codelutin.com March 20, 2012

March 20, 2012

Author: echatellier Date: 2012-03-20 09:58:26 +0100 (Tue, 20 Mar 2012) New Revision: 3664 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3664 Log: Fix all import/export tests Added: branches/4.0.1/src/test/resources/mexico/mexicohelper_designplanV3.xml Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DiscreteDomainXMLVisitor.java branches/4.0.1/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DiscreteDomainXMLVisitor.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DiscreteDomainXMLVisitor.java 2012-03-19 17:45:36 UTC (rev 3663) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DiscreteDomainXMLVisitor.java 2012-03-20 08:58:26 UTC (rev 3664) @@ -27,6 +27,7 @@ import fr.ifremer.isisfish.mexico.MexicoHelper; import fr.ifremer.isisfish.simulator.sensitivity.Domain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; /** * XML discrete domain visitor. @@ -44,9 +45,26 @@ */ @Override public void start(Domain domain) { + DiscreteDomain discreteDomain = (DiscreteDomain)domain; + // lorsque le facteur est catégoriel, la liste de ses niveaux, par une // liste ouverte d'éléments 'level', d'attributs 'value' et 'weight') - xmlBuffer.append("<domain distributionName=\"categorical\" type=\"discretetruc\">"); + xmlBuffer.append("<domain distributionName=\"categorical\" type=\""); + + if (!discreteDomain.getValues().isEmpty()) { + Object first = discreteDomain.getValues().firstKey(); + Object firstValue = discreteDomain.getValues().get(first); + + if (firstValue instanceof Integer) { + xmlBuffer.append("integer"); + } else if (firstValue instanceof Double) { + xmlBuffer.append("double"); + } else { + xmlBuffer.append("string"); + } + } + + xmlBuffer.append("\">"); } /** Modified: branches/4.0.1/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java =================================================================== --- branches/4.0.1/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java 2012-03-19 17:45:36 UTC (rev 3663) +++ branches/4.0.1/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java 2012-03-20 08:58:26 UTC (rev 3664) @@ -378,9 +378,11 @@ @Test public void testExportImportWithGroup() throws IOException, IsisFishException, TopiaException { + Date date = new Date(); + // first export DesignPlan testDesignPlan = getTestDesignPlan(true, false); - String xml1 = MexicoHelper.getDesignPlanAsXML(testDesignPlan); + String xml1 = MexicoHelper.getDesignPlanAsXML(testDesignPlan, "date", date.toString()); if (log.isDebugEnabled()) { log.debug("xml 1 = " + xml1); } @@ -391,7 +393,7 @@ TopiaContext context = regionContext.beginTransaction(); DesignPlan plan = MexicoHelper.getDesignPlanFromXML(testFile, context); context.closeContext(); - String xml2 = MexicoHelper.getDesignPlanAsXML(plan); + String xml2 = MexicoHelper.getDesignPlanAsXML(plan, "date", date.toString()); if (log.isDebugEnabled()) { log.debug("xml 2 = " + xml2); } @@ -596,9 +598,11 @@ /** * Test que le xml généré est valide avec la xsd mexico (exp design). * + * Test is currently disabled, isis fish doesn't respect all mexico + * file format since it's not possible. + * * @throws Exception */ - //@Test public void validOutputXml() throws Exception { DesignPlan testDesignPlan = getTestDesignPlan(true, true); Added: branches/4.0.1/src/test/resources/mexico/mexicohelper_designplanV3.xml =================================================================== (Binary files differ) Property changes on: branches/4.0.1/src/test/resources/mexico/mexicohelper_designplanV3.xml ___________________________________________________________________ Added: svn:mime-type + application/xml

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r3663 - in branches/4.0.1/src: main/java/fr/ifremer/isisfish/mexico/xml test/java/fr/ifremer/isisfish/mexico test/resources/mexico
by echatellier＠users.forge.codelutin.com March 19, 2012

March 19, 2012

Author: echatellier Date: 2012-03-19 18:45:36 +0100 (Mon, 19 Mar 2012) New Revision: 3663 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3663 Log: Fix more tests Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DiscreteDomainXMLVisitor.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/EquationDiscreteDomainXMLVisitor.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/RuleDiscreteDomainXMLVisitor.java branches/4.0.1/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java branches/4.0.1/src/test/resources/mexico/mexicohelper_designplan.xml branches/4.0.1/src/test/resources/mexico/mexicohelper_designplanV2.xml branches/4.0.1/src/test/resources/mexico/mexicohelper_factorgroupdp.xml Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DiscreteDomainXMLVisitor.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DiscreteDomainXMLVisitor.java 2012-03-19 16:39:55 UTC (rev 3662) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DiscreteDomainXMLVisitor.java 2012-03-19 17:45:36 UTC (rev 3663) @@ -54,7 +54,7 @@ */ @Override public void visit(Domain domain, Object label, Object value) { - xmlBuffer.append("<level name=\"" + label + "\">"); + xmlBuffer.append("<level>"); xmlBuffer.append(MexicoHelper.getStringFromObject(value)); xmlBuffer.append("</level>"); } Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java 2012-03-19 16:39:55 UTC (rev 3662) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java 2012-03-19 17:45:36 UTC (rev 3663) @@ -42,7 +42,6 @@ import fr.ifremer.isisfish.simulator.sensitivity.DesignPlan; import fr.ifremer.isisfish.simulator.sensitivity.Distribution; import fr.ifremer.isisfish.simulator.sensitivity.Distribution.DistributionParam; -import fr.ifremer.isisfish.simulator.sensitivity.Domain; import fr.ifremer.isisfish.simulator.sensitivity.Factor; import fr.ifremer.isisfish.simulator.sensitivity.FactorGroup; import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; @@ -144,20 +143,19 @@ // matrix specific // <coefficient operator="-" value="0.799"/> domain = new ContinuousDomain(Distribution.QUNIFPC); - Element coefficientElement = fixedElement.element("coefficient"); - domain.addDistributionParam("coefficient", Double.valueOf(coefficientElement.attributeValue("value"))); // <mx name="test1" step="0">... Element matrixElement = fixedElement.element("mx"); MatrixND matrix = MexicoHelper.getMatrixFromXml(matrixElement, topiaContext); domain.addDistributionParam("reference", matrix); + + Element coefficientElement = fixedElement.element("coefficient"); + domain.addDistributionParam("coefficient", Double.valueOf(coefficientElement.attributeValue("value"))); } else if (property.equals("equationcontinuous")) { // equation specific domain = new ContinuousDomain(Distribution.QUNIFPC); - Element coefficientElement = fixedElement.element("coefficient"); - domain.addDistributionParam("coefficient", Double.valueOf(coefficientElement.attributeValue("value"))); - + Element equationElement = fixedElement.element("equation"); domain.addDistributionParam("reference", Double.valueOf(equationElement.attributeValue("reference"))); String variable = equationElement.attributeValue("variable"); @@ -165,7 +163,11 @@ // hack since 4.0.1, factor name doesn't contains variable name = StringUtils.removeEnd(name, "." + variable); factor.setName(name); + + Element coefficientElement = fixedElement.element("coefficient"); + domain.addDistributionParam("coefficient", Double.valueOf(coefficientElement.attributeValue("value"))); + } else { // continous domain @@ -173,8 +175,8 @@ Element percentageElement = fixedElement.element("percentage"); if (percentageElement != null) { domain = new ContinuousDomain(Distribution.QUNIFPC); + domain.addDistributionParam("reference", Double.valueOf(percentageElement.attributeValue("reference"))); domain.addDistributionParam("coefficient", Double.valueOf(percentageElement.attributeValue("coefficient"))); - domain.addDistributionParam("reference", Double.valueOf(percentageElement.attributeValue("reference"))); } else { // <range max="1.0" min="0.0"/> @@ -210,19 +212,17 @@ // matrix specific domain = new ContinuousDomain(Distribution.QUNIFPC); - Element coefficientElement = fixedElement.element("coefficient"); - domain.addDistributionParam("coefficient", Double.valueOf(coefficientElement.attributeValue("value"))); - // matrix specific Element matrixElement = fixedElement.element("mx"); MatrixND matrix = MexicoHelper.getMatrixFromXml(matrixElement, topiaContext); domain.addDistributionParam("reference", matrix); + + Element coefficientElement = fixedElement.element("coefficient"); + domain.addDistributionParam("coefficient", Double.valueOf(coefficientElement.attributeValue("value"))); } else if (property.equals("equationcontinuous")) { // equation specific domain = new ContinuousDomain(Distribution.QUNIFPC); - Element coefficientElement = fixedElement.element("coefficient"); - domain.addDistributionParam("coefficient", Double.valueOf(coefficientElement.attributeValue("value"))); Element equationElement = fixedElement.element("equation"); domain.addDistributionParam("reference", Double.valueOf(equationElement.attributeValue("reference"))); @@ -231,14 +231,17 @@ // hack since 4.0.1, factor name doesn't contains variable name = StringUtils.removeEnd(name, "." + variable); factor.setName(name); + + Element coefficientElement = fixedElement.element("coefficient"); + domain.addDistributionParam("coefficient", Double.valueOf(coefficientElement.attributeValue("value"))); } else { // continous domain Element percentageElement = fixedElement.element("percentage"); if (percentageElement != null) { domain = new ContinuousDomain(Distribution.QUNIFPC); + domain.addDistributionParam("reference", Double.valueOf(percentageElement.attributeValue("reference"))); domain.addDistributionParam("coefficient", Double.valueOf(percentageElement.attributeValue("coefficient"))); - domain.addDistributionParam("reference", Double.valueOf(percentageElement.attributeValue("reference"))); } else { // <range max="1" min="3"/> @@ -346,11 +349,12 @@ domain = new ContinuousDomain(Distribution.QUNIFPC); // matrix specific // <coefficient operator="-" value="0.799"/> - domain.addDistributionParam("coefficient", Double.valueOf(referenceElement.attributeValue("coefficient"))); // <mx name="test1" step="0">... Element matrixElement = referenceElement.element("mx"); MatrixND matrix = MexicoHelper.getMatrixFromXml(matrixElement, topiaContext); domain.addDistributionParam("reference", matrix); + + domain.addDistributionParam("coefficient", Double.valueOf(referenceElement.attributeValue("coefficient"))); } else { domain = new ContinuousDomain(Distribution.QUNIFMM); @@ -363,7 +367,7 @@ domain.addDistributionParam("max", maxMatrix); } } - else if (property.equals("equationcontinuos")) { + else if (property.equals("equationcontinuous")) { // equation specific String variable = fixedElement.attributeValue("variable"); @@ -375,8 +379,8 @@ Element referenceElement = fixedElement.element("reference"); if (referenceElement != null) { domain = new ContinuousDomain(Distribution.QUNIFPC); + domain.addDistributionParam("reference", Double.valueOf(referenceElement.getTextTrim())); domain.addDistributionParam("coefficient", Double.valueOf(referenceElement.attributeValue("coefficient"))); - domain.addDistributionParam("reference", Double.valueOf(referenceElement.getTextTrim())); } else { domain = new ContinuousDomain(Distribution.QUNIFMM); @@ -392,8 +396,8 @@ Element referenceElement = fixedElement.element("reference"); if (referenceElement != null) { domain = new ContinuousDomain(Distribution.QUNIFPC); + domain.addDistributionParam("reference", Double.valueOf(referenceElement.getTextTrim())); domain.addDistributionParam("coefficient", Double.valueOf(referenceElement.attributeValue("coefficient"))); - domain.addDistributionParam("reference", Double.valueOf(referenceElement.getTextTrim())); } else { // <range max="1.0" min="0.0"/> @@ -436,11 +440,11 @@ domain = new ContinuousDomain(Distribution.QUNIFPC); // matrix specific // <coefficient operator="-" value="0.799"/> - domain.addDistributionParam("coefficient", Double.valueOf(referenceElement.attributeValue("coefficient"))); // <mx name="test1" step="0">... Element matrixElement = referenceElement.element("mx"); MatrixND matrix = MexicoHelper.getMatrixFromXml(matrixElement, topiaContext); domain.addDistributionParam("reference", matrix); + domain.addDistributionParam("coefficient", Double.valueOf(referenceElement.attributeValue("coefficient"))); } else { domain = new ContinuousDomain(Distribution.QUNIFMM); @@ -464,8 +468,8 @@ Element referenceElement = fixedElement.element("reference"); if (referenceElement != null) { domain = new ContinuousDomain(Distribution.QUNIFPC); + domain.addDistributionParam("reference", Double.valueOf(referenceElement.getTextTrim())); domain.addDistributionParam("coefficient", Double.valueOf(referenceElement.attributeValue("coefficient"))); - domain.addDistributionParam("reference", Double.valueOf(referenceElement.getTextTrim())); } else { domain = new ContinuousDomain(Distribution.QUNIFMM); @@ -481,8 +485,8 @@ Element referenceElement = fixedElement.element("reference"); if (referenceElement != null) { domain = new ContinuousDomain(Distribution.QUNIFPC); + domain.addDistributionParam("reference", Double.valueOf(referenceElement.getTextTrim())); domain.addDistributionParam("coefficient", Double.valueOf(referenceElement.attributeValue("coefficient"))); - domain.addDistributionParam("reference", Double.valueOf(referenceElement.getTextTrim())); } else { // <range max="1.0" min="0.0"/> @@ -631,32 +635,39 @@ List<Element> levelElements = domainElement.elements("level"); if ("rule".equals(type)) { domain = new RuleDiscreteDomain(); + int valueName = 0; for (Element levelElement : levelElements) { - String levelName = levelElement.attributeValue("name"); Element rulesElement = levelElement.element("rules"); List<Rule> rulesValue = MexicoHelper.getRulesFromXml(rulesElement, topiaContext); - domain.getValues().put(levelName, rulesValue); + domain.getValues().put(valueName++, rulesValue); } + } else if ("equation".equals(type)) { // topia entities ... + domain = new EquationDiscreteDomain(); + int valueName = 0; + for (Element levelElement : levelElements) { // no trim here + Object object = StringEscapeUtils.unescapeXml(levelElement.getText()); + domain.getValues().put(valueName++, object); + } } else if ("string".equals(type)) { // topia entities ... domain = new DiscreteDomain(); + int valueName = 0; for (Element levelElement : levelElements) { - String levelName = levelElement.attributeValue("name"); Object object = MexicoHelper.getObjectFromString(levelElement.getTextTrim(), topiaContext); - domain.getValues().put(levelName, object); + domain.getValues().put(valueName++, object); } } else if ("integer".equals(type)) { domain = new DiscreteDomain(); + int valueName = 0; for (Element levelElement : levelElements) { - String levelName = levelElement.attributeValue("name"); Integer levelValue = Integer.valueOf(levelElement.getTextTrim()); - domain.getValues().put(levelName, levelValue); + domain.getValues().put(valueName++, levelValue); } } else { domain = new DiscreteDomain(); + int valueName = 0; for (Element levelElement : levelElements) { - String levelName = levelElement.attributeValue("name"); Double levelValue = Double.valueOf(levelElement.getTextTrim()); - domain.getValues().put(levelName, levelValue); + domain.getValues().put(valueName++, levelValue); } } Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/EquationDiscreteDomainXMLVisitor.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/EquationDiscreteDomainXMLVisitor.java 2012-03-19 16:39:55 UTC (rev 3662) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/EquationDiscreteDomainXMLVisitor.java 2012-03-19 17:45:36 UTC (rev 3663) @@ -44,7 +44,7 @@ public void start(Domain domain) { // lorsque le facteur est catégoriel, la liste de ses niveaux, par une // liste ouverte d'éléments 'level', d'attributs 'value' et 'weight') - xmlBuffer.append("<domain distributionName=\"categorical\" type=\"equation\""); + xmlBuffer.append("<domain distributionName=\"categorical\" type=\"equation\">"); } /** @@ -53,8 +53,8 @@ @Override public void visit(Domain domain, Object label, Object value) { String content = (String)value; - xmlBuffer.append("<value>"); + xmlBuffer.append("<level>"); xmlBuffer.append(StringEscapeUtils.escapeXml(content)); - xmlBuffer.append("</value>"); + xmlBuffer.append("</level>"); } } Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/RuleDiscreteDomainXMLVisitor.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/RuleDiscreteDomainXMLVisitor.java 2012-03-19 16:39:55 UTC (rev 3662) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/RuleDiscreteDomainXMLVisitor.java 2012-03-19 17:45:36 UTC (rev 3663) @@ -57,7 +57,7 @@ List<Rule> rulesList = (List<Rule>)value; String rulesAsXml = MexicoHelper.getRulesAsXml(rulesList); - xmlBuffer.append("<level name=\"" + label + "\">"); + xmlBuffer.append("<level>"); xmlBuffer.append(rulesAsXml); xmlBuffer.append("</level>"); } Modified: branches/4.0.1/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java =================================================================== --- branches/4.0.1/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java 2012-03-19 16:39:55 UTC (rev 3662) +++ branches/4.0.1/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java 2012-03-19 17:45:36 UTC (rev 3663) @@ -138,7 +138,7 @@ Factor factorContinuous = new Factor("factor 1 (double continuous)"); ContinuousDomain domain1 = new ContinuousDomain(Distribution.QUNIFMM); domain1.addDistributionParam("min", 0.0); - domain1.addDistributionParam("max", 0.0); + domain1.addDistributionParam("max", 50.0); factorContinuous.setDomain(domain1); factorContinuous.setPath("fr.ifremer.isisfish.entities.PopulationGroup#1156461521013#0.1715620681984218#maxLength"); @@ -175,8 +175,8 @@ Factor factorEquationContinuous = new Factor("factor 5 (EquationContinuous)"); factorEquationContinuous.setEquationVariableName("Ktemp"); ContinuousDomain domain5 = new ContinuousDomain(Distribution.QUNIFPC); - domain5.addDistributionParam("reference", 0.1); - domain5.addDistributionParam("coefficient", 45.0); + domain5.addDistributionParam("reference", 45.0); + domain5.addDistributionParam("coefficient", 0.1); factorEquationContinuous.setDomain(domain5); factorEquationContinuous.setPath("fr.ifremer.isisfish.entities.PopulationGroup#1156461521076#0.6526656643346673#maxLength"); @@ -256,25 +256,26 @@ // test xml export String xml = MexicoHelper.getDesignPlanAsXML(testDesignPlan); + if (log.isDebugEnabled()) { + log.debug("testGetDesignPlanAsXML xml = " + xml); + } + // factor 1 - Assert.assertTrue(xml.contains("<min>0.0</min>")); - Assert.assertTrue(xml.contains("<max>50.0</max>")); + Assert.assertTrue(xml.contains("distributionParameter name=\"min\" type=\"decimal\">0.0")); + Assert.assertTrue(xml.contains("distributionParameter name=\"max\" type=\"decimal\">50.0")); // factor 2 - Assert.assertTrue(xml.contains("<factor name=\"factor 2 (double discrete)\"")); - Assert.assertTrue(xml.contains("<value>70.9</value>")); + Assert.assertTrue(xml.contains("name=\"factor 2 (double discrete)\"")); + Assert.assertTrue(xml.contains("<level>70.9</level>")); // factor 3 - Assert.assertTrue(xml.contains("<value>14</value>")); + Assert.assertTrue(xml.contains("<level>14</level>")); // factor 4 Assert.assertTrue(xml.contains("<d>-14.0</d>")); Assert.assertTrue(xml.contains("0.799")); Assert.assertTrue(xml.contains("<mx name=\"test1\">")); // factor 5 - Assert.assertTrue(xml.contains("<fixed variable=\"L1\">")); - Assert.assertTrue(xml.contains("<reference coefficient=\"0.1\">45.0</reference>")); - - if (log.isDebugEnabled()) { - log.debug("testGetDesignPlanAsXML xml = " + xml); - } + Assert.assertTrue(xml.contains("name=\"equationVariableName\">Ktemp")); + Assert.assertTrue(xml.contains("distributionParameter name=\"coefficient\" type=\"decimal\">0.1")); + Assert.assertTrue(xml.contains("distributionParameter name=\"reference\" type=\"decimal\">45.0")); } /** @@ -350,19 +351,21 @@ // test xml export String xml = MexicoHelper.getDesignPlanAsXML(testDesignPlan); + if (log.isDebugEnabled()) { + log.debug("testFactorGroupAndRule xml = " + xml); + } + // factor groups - Assert.assertTrue(xml.indexOf("<factors name=\"continuousgrp\" type=\"continuous\">") != -1); - Assert.assertTrue(xml.indexOf("<factors name=\"discretegrp\" type=\"discrete\">") != -1); + Assert.assertTrue(xml.indexOf("<feature name=\"group\">continuousgrp") != -1); + Assert.assertTrue(xml.indexOf("<feature name=\"grouptype\">continuous") != -1); + Assert.assertTrue(xml.indexOf("<feature name=\"group\">discretegrp") != -1); + Assert.assertTrue(xml.indexOf("<feature name=\"group\">discrete") != -1); // factor 6 Assert.assertTrue(xml.indexOf("<rule name=\"TACpoids\">") != -1); Assert.assertTrue(xml.indexOf("<rule name=\"TailleMin\">") != -1); Assert.assertTrue(xml.indexOf("<param key=\"rule.0.parameter.propSurvie\">42.0</param>") != -1); Assert.assertTrue(xml.indexOf("<param key=\"rule.0.parameter.species\">fr.ifremer.isisfish.entities.Species#1169028645830#0.022262364425031378</param>") != -1); - - if (log.isDebugEnabled()) { - log.debug("testFactorGroupAndRule xml = " + xml); - } } /** @@ -381,7 +384,6 @@ if (log.isDebugEnabled()) { log.debug("xml 1 = " + xml1); } - System.out.println(xml1); // export File testFile = new File("src/test/resources/mexico/mexicohelper_factorgroupdp.xml"); @@ -412,16 +414,16 @@ // test xml export String xml = MexicoHelper.getDesignPlanAsXML(testDesignPlan); + if (log.isDebugEnabled()) { + log.debug("testFactorRuleParams xml = " + xml); + } + // factor groups Assert.assertTrue(xml.indexOf("type=\"string\"") != -1); // factor 8 - Assert.assertTrue(xml.indexOf("<value>Strategy:PelProfil1</value>") != -1); - Assert.assertTrue(xml.indexOf("<value>Strategy:PelProfil2</value>") != -1); - - if (log.isDebugEnabled()) { - log.debug("testFactorRuleParams xml = " + xml); - } + Assert.assertTrue(xml.indexOf("<level>Strategy:PelProfil1</level>") != -1); + Assert.assertTrue(xml.indexOf("<level>Strategy:PelProfil2</level>") != -1); } /** @@ -454,7 +456,7 @@ Factor factorMatrixContinuous = new Factor("factor x4"); ContinuousDomain domain4 = new ContinuousDomain(Distribution.QUNIFMM); domain4.addDistributionParam("min", matrix1); - domain4.addDistributionParam("min", matrix1); + domain4.addDistributionParam("max", matrix1); factorMatrixContinuous.setDomain(domain4); factorMatrixContinuous.setPath("fr.ifremer.isisfish.entities.PopulationGroup#1156461521076#0.6526656643346673#minLength"); @@ -507,8 +509,9 @@ testDesignPlan.addFactor(factorEquationDiscrete); + Date date = new Date(); // test write - String content = MexicoHelper.getDesignPlanAsXML(testDesignPlan); + String content = MexicoHelper.getDesignPlanAsXML(testDesignPlan, "date", date.toString()); Assert.assertTrue(content.contains("context.getValue() < 1.0")); File tempFile = File.createTempFile("testdesignplan", ".xml"); @@ -517,7 +520,7 @@ // test to read it and get content DesignPlan plan = MexicoHelper.getDesignPlanFromXML(tempFile, null); - String reReadContent = MexicoHelper.getDesignPlanAsXML(plan); + String reReadContent = MexicoHelper.getDesignPlanAsXML(plan, "date", date.toString()); Assert.assertEquals(content, reReadContent); } @@ -533,9 +536,11 @@ @Test public void testExportImportV2() throws IOException, IsisFishException, TopiaException { + Date date = new Date(); + // first export DesignPlan testDesignPlan = getTestDesignPlan(false, false); - String xml1 = MexicoHelper.getDesignPlanAsXML(testDesignPlan); + String xml1 = MexicoHelper.getDesignPlanAsXML(testDesignPlan, "date", date.toString()); if (log.isDebugEnabled()) { log.debug("xml 1 = " + xml1); } @@ -544,7 +549,7 @@ File testFile = new File("src/test/resources/mexico/mexicohelper_designplanV2.xml"); // topia context can be null in tests DesignPlan plan = MexicoHelper.getDesignPlanFromXML(testFile, regionContext); - String xml2 = MexicoHelper.getDesignPlanAsXML(plan); + String xml2 = MexicoHelper.getDesignPlanAsXML(plan, "date", date.toString()); if (log.isDebugEnabled()) { log.debug("xml 2 = " + xml2); } Modified: branches/4.0.1/src/test/resources/mexico/mexicohelper_designplan.xml =================================================================== --- branches/4.0.1/src/test/resources/mexico/mexicohelper_designplan.xml 2012-03-19 16:39:55 UTC (rev 3662) +++ branches/4.0.1/src/test/resources/mexico/mexicohelper_designplan.xml 2012-03-19 17:45:36 UTC (rev 3663) @@ -93,7 +93,7 @@ <fixed cardinality="0"> <range max="1.0" min="0.0"/> <coefficient operator="-" value="0.1"/> - <equation reference="45.0" variable="L1"/> + <equation reference="45.0" variable="Ktemp"/> </fixed> </domain> </factor> Modified: branches/4.0.1/src/test/resources/mexico/mexicohelper_designplanV2.xml =================================================================== --- branches/4.0.1/src/test/resources/mexico/mexicohelper_designplanV2.xml 2012-03-19 16:39:55 UTC (rev 3662) +++ branches/4.0.1/src/test/resources/mexico/mexicohelper_designplanV2.xml 2012-03-19 17:45:36 UTC (rev 3663) @@ -92,7 +92,7 @@ <factor name="factor 5 (EquationContinuous)" property="equationcontinuous" type="real" cardinality="0"> <target>fr.ifremer.isisfish.entities.PopulationGroup#1156461521076#0.6526656643346673#maxLength</target> <domain> - <fixed variable="L1"> + <fixed variable="Ktemp"> <reference coefficient="0.1">45.0</reference> </fixed> </domain> Modified: branches/4.0.1/src/test/resources/mexico/mexicohelper_factorgroupdp.xml =================================================================== --- branches/4.0.1/src/test/resources/mexico/mexicohelper_factorgroupdp.xml 2012-03-19 16:39:55 UTC (rev 3662) +++ branches/4.0.1/src/test/resources/mexico/mexicohelper_factorgroupdp.xml 2012-03-19 17:45:36 UTC (rev 3663) @@ -67,7 +67,7 @@ <factor name="factor 5 (EquationContinuous)" property="equationcontinuous" type="real" cardinality="0"> <target>fr.ifremer.isisfish.entities.PopulationGroup#1156461521076#0.6526656643346673#maxLength</target> <domain> - <fixed variable="L1"> + <fixed variable="Ktemp"> <reference coefficient="0.1">45.0</reference> </fixed> </domain>

1 0

r3662 - branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain
by echatellier＠users.forge.codelutin.com March 19, 2012

March 19, 2012

Author: echatellier Date: 2012-03-19 17:39:55 +0100 (Mon, 19 Mar 2012) New Revision: 3662 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3662 Log: Parameters are not sorted anymore (bad idea, not sorted in xml files too) 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 2012-03-19 16:12:45 UTC (rev 3661) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java 2012-03-19 16:39:55 UTC (rev 3662) @@ -25,9 +25,10 @@ package fr.ifremer.isisfish.simulator.sensitivity.domain; +import java.util.HashMap; +import java.util.Map; import java.util.Map.Entry; import java.util.SortedMap; -import java.util.TreeMap; import fr.ifremer.isisfish.IsisFishRuntimeException; import fr.ifremer.isisfish.simulator.sensitivity.Distribution; @@ -53,7 +54,7 @@ protected Distribution distribution; /** Distribution params (param name > param value). */ - protected SortedMap<String, Object> distributionParameters = new TreeMap<String, Object>(); + protected Map<String, Object> distributionParameters = new HashMap<String, Object>(); /** * Default constructor. @@ -97,7 +98,7 @@ * * @return distribution parameters */ - public SortedMap<String, Object> getDistributionParameters() { + public Map<String, Object> getDistributionParameters() { return distributionParameters; } @@ -137,10 +138,16 @@ } // get current parameter definition - DistributionParam defDistribParams = distribution.getDistibutionParams()[distributionParameters.size()]; - if (!defDistribParams.getName().equals(name)) { - throw new IllegalArgumentException(String.format("Wrong parameter name, expected %s, got %s", defDistribParams.getName(), name)); + boolean found = false; + DistributionParam[] defDistribParams = distribution.getDistibutionParams(); + for (DistributionParam defDistribParam : defDistribParams) { + if (defDistribParam.getName().equals(name)) { + found = true; + } } + if (!found) { + throw new IllegalArgumentException(String.format("Wrong parameter name, %s not supported by distribution", name)); + } distributionParameters.put(name, value); }

1 0

r3661 - branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml
by echatellier＠users.forge.codelutin.com March 19, 2012

March 19, 2012

Author: echatellier Date: 2012-03-19 17:12:45 +0100 (Mon, 19 Mar 2012) New Revision: 3661 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3661 Log: Fix v3 import/export test Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/ContinuousDomainXMLVisitor.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DiscreteDomainXMLVisitor.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/ContinuousDomainXMLVisitor.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/ContinuousDomainXMLVisitor.java 2012-03-19 15:41:02 UTC (rev 3660) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/ContinuousDomainXMLVisitor.java 2012-03-19 16:12:45 UTC (rev 3661) @@ -71,7 +71,7 @@ xmlBuffer.append(" type=\"matrix\">"); xmlBuffer.append(MexicoHelper.getMatrixAsXML((MatrixND)value)); } else { - xmlBuffer.append(" type=\"double\">"); + xmlBuffer.append(" type=\"decimal\">"); xmlBuffer.append(value.toString()); } } Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DiscreteDomainXMLVisitor.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DiscreteDomainXMLVisitor.java 2012-03-19 15:41:02 UTC (rev 3660) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DiscreteDomainXMLVisitor.java 2012-03-19 16:12:45 UTC (rev 3661) @@ -46,7 +46,7 @@ public void start(Domain domain) { // lorsque le facteur est catégoriel, la liste de ses niveaux, par une // liste ouverte d'éléments 'level', d'attributs 'value' et 'weight') - xmlBuffer.append("<domain distributionName=\"categorical\" type=\"todo\">"); + xmlBuffer.append("<domain distributionName=\"categorical\" type=\"discretetruc\">"); } /** Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java 2012-03-19 15:41:02 UTC (rev 3660) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java 2012-03-19 16:12:45 UTC (rev 3661) @@ -41,6 +41,7 @@ import fr.ifremer.isisfish.rule.Rule; import fr.ifremer.isisfish.simulator.sensitivity.DesignPlan; import fr.ifremer.isisfish.simulator.sensitivity.Distribution; +import fr.ifremer.isisfish.simulator.sensitivity.Distribution.DistributionParam; import fr.ifremer.isisfish.simulator.sensitivity.Domain; import fr.ifremer.isisfish.simulator.sensitivity.Factor; import fr.ifremer.isisfish.simulator.sensitivity.FactorGroup; @@ -612,6 +613,10 @@ if (groupTypeElement != null) { groupType = groupTypeElement.getTextTrim(); } + Element varNameElement = (Element)factorElement.selectSingleNode("child::feature[@name='equationVariableName']"); + if (varNameElement != null) { + factor.setEquationVariableName(varNameElement.getTextTrim()); + } // parse domain @@ -621,27 +626,36 @@ // facteur discret if ("categorical".equals(distributionName)) { - DiscreteDomain domain = new DiscreteDomain(); + DiscreteDomain domain; List<Element> levelElements = domainElement.elements("level"); if ("rule".equals(type)) { - int label = 0; + domain = new RuleDiscreteDomain(); for (Element levelElement : levelElements) { + String levelName = levelElement.attributeValue("name"); Element rulesElement = levelElement.element("rules"); List<Rule> rulesValue = MexicoHelper.getRulesFromXml(rulesElement, topiaContext); - domain.getValues().put(label, rulesValue); - ++label; + domain.getValues().put(levelName, rulesValue); } } else if ("string".equals(type)) { // topia entities ... + domain = new DiscreteDomain(); for (Element levelElement : levelElements) { String levelName = levelElement.attributeValue("name"); Object object = MexicoHelper.getObjectFromString(levelElement.getTextTrim(), topiaContext); domain.getValues().put(levelName, object); } + } else if ("integer".equals(type)) { + domain = new DiscreteDomain(); + for (Element levelElement : levelElements) { + String levelName = levelElement.attributeValue("name"); + Integer levelValue = Integer.valueOf(levelElement.getTextTrim()); + domain.getValues().put(levelName, levelValue); + } } else { + domain = new DiscreteDomain(); for (Element levelElement : levelElements) { String levelName = levelElement.attributeValue("name"); - Double levelValue = Double.parseDouble(levelElement.getTextTrim()); + Double levelValue = Double.valueOf(levelElement.getTextTrim()); domain.getValues().put(levelName, levelValue); } } @@ -667,8 +681,11 @@ ContinuousDomain domain = new ContinuousDomain(distribution); - List<Element> paramElements = domainElement.elements("distributionParameter"); - for (Element paramElement : paramElements) { + // ne tient pas compte de l'ordre des parametres + // dans le fichier xml + DistributionParam[] paramsDef = distribution.getDistibutionParams(); + for (DistributionParam paramDef : paramsDef) { + Element paramElement = (Element)domainElement.selectSingleNode("distributionParameter[@name='" + paramDef.getName() + "']"); String paramName = paramElement.attributeValue("name"); String paramType = paramElement.attributeValue("type");

1 0

r3660 - in branches/4.0.1/src: main/java/fr/ifremer/isisfish/mexico/xml test/java/fr/ifremer/isisfish/mexico
by echatellier＠users.forge.codelutin.com March 19, 2012

March 19, 2012

Author: echatellier Date: 2012-03-19 16:41:02 +0100 (Mon, 19 Mar 2012) New Revision: 3660 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3660 Log: Fix mexico file format parsing Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/ContinuousDomainXMLVisitor.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DesignPlanXMLVisitor.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DiscreteDomainXMLVisitor.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/FactorXMLVisitor.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/RuleDiscreteDomainXMLVisitor.java branches/4.0.1/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/ContinuousDomainXMLVisitor.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/ContinuousDomainXMLVisitor.java 2012-03-15 17:43:01 UTC (rev 3659) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/ContinuousDomainXMLVisitor.java 2012-03-19 15:41:02 UTC (rev 3660) @@ -50,7 +50,7 @@ @Override public void start(Domain domain) { ContinuousDomain cDomain = (ContinuousDomain)domain; - xmlBuffer.append("<domain distribution=\"" + cDomain.getDistribution().toString().toLowerCase() + "\">"); + xmlBuffer.append("<domain distributionName=\"" + cDomain.getDistribution().toString().toLowerCase() + "\">"); for (Entry<String, Object> distributionParameterEntry : cDomain.getDistributionParameters().entrySet()) { String name = distributionParameterEntry.getKey(); Object value = distributionParameterEntry.getValue(); Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DesignPlanXMLVisitor.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DesignPlanXMLVisitor.java 2012-03-15 17:43:01 UTC (rev 3659) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DesignPlanXMLVisitor.java 2012-03-19 15:41:02 UTC (rev 3660) @@ -70,7 +70,7 @@ xmlBuffer.append("<experimentalDesign"); // for validation (tests) - xmlBuffer.append(" xmlns='http://www.reseau-mexico.fr/sites/reseau-mexico.fr/files/expDesign.xsd'"); + //xmlBuffer.append(" xmlns='http://www.reseau-mexico.fr/sites/reseau-mexico.fr/files/expDesign.xsd'"); xmlBuffer.append(" version=\"3\""); xmlBuffer.append(" author=\"" + (authorIndex != -1 ? args[authorIndex + 1] : "") + "\""); xmlBuffer.append(" license=\"" + (licenseIndex != -1 ? args[licenseIndex + 1] : "") + "\""); Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DiscreteDomainXMLVisitor.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DiscreteDomainXMLVisitor.java 2012-03-15 17:43:01 UTC (rev 3659) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DiscreteDomainXMLVisitor.java 2012-03-19 15:41:02 UTC (rev 3660) @@ -46,7 +46,7 @@ public void start(Domain domain) { // lorsque le facteur est catégoriel, la liste de ses niveaux, par une // liste ouverte d'éléments 'level', d'attributs 'value' et 'weight') - xmlBuffer.append("<domain distributionName=\"categorical\" type=\"todo\""); + xmlBuffer.append("<domain distributionName=\"categorical\" type=\"todo\">"); } /** Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java 2012-03-15 17:43:01 UTC (rev 3659) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java 2012-03-19 15:41:02 UTC (rev 3660) @@ -78,7 +78,7 @@ // could return "2" or null String version = rootElement.attributeValue("version"); - List<Element> factorGroupElements = rootElement.selectNodes("child::factors"); + List<Element> factorGroupElements = rootElement.elements("factors"); FactorGroup factorGroup = null; if (!factorGroupElements.isEmpty()) { if ("3".equals(version)) { @@ -588,30 +588,66 @@ Map<String, FactorGroup> groups = new HashMap<String, FactorGroup>(); // normal factors - List<Element> factorElements = fgElement.selectNodes("child::factor"); + List<Element> factorElements = fgElement.elements("factor"); for (Element factorElement : factorElements) { String name = factorElement.attributeValue("name"); - String cardinalityString = fgElement.element("child::feature[@name='cardinality']").getTextTrim(); - String path = fgElement.element("child::feature[@name='target']").getTextTrim(); - String groupName = fgElement.element("child::feature[@name='group']").getTextTrim(); - String groupType = fgElement.element("child::feature[@name='grouptype']").getTextTrim(); + String groupName = null; + String groupType = null; Factor factor = new Factor(name); - factor.setPath(path); - if (StringUtils.isNotEmpty(cardinalityString)) { - factor.setCardinality(Integer.valueOf(cardinalityString)); + + Element cardinalityElement = (Element)factorElement.selectSingleNode("child::feature[@name='cardinality']"); + if (cardinalityElement != null) { + factor.setCardinality(Integer.valueOf(cardinalityElement.getTextTrim())); } + Element targetElement = (Element)factorElement.selectSingleNode("child::feature[@name='target']"); + if (targetElement != null) { + factor.setPath(targetElement.getTextTrim()); + } + Element groupElement = (Element)factorElement.selectSingleNode("child::feature[@name='group']"); + if (groupElement != null) { + groupName = groupElement.getTextTrim(); + } + Element groupTypeElement = (Element)factorElement.selectSingleNode("child::feature[@name='grouptype']"); + if (groupTypeElement != null) { + groupType = groupTypeElement.getTextTrim(); + } + // parse domain Element domainElement = factorElement.element("domain"); String distributionName = domainElement.attributeValue("distributionName"); String type = domainElement.attributeValue("type"); - Domain domain; + // facteur discret if ("categorical".equals(distributionName)) { + DiscreteDomain domain = new DiscreteDomain(); + + List<Element> levelElements = domainElement.elements("level"); if ("rule".equals(type)) { - + int label = 0; + for (Element levelElement : levelElements) { + Element rulesElement = levelElement.element("rules"); + List<Rule> rulesValue = MexicoHelper.getRulesFromXml(rulesElement, topiaContext); + domain.getValues().put(label, rulesValue); + ++label; + } + } else if ("string".equals(type)) { // topia entities ... + for (Element levelElement : levelElements) { + String levelName = levelElement.attributeValue("name"); + Object object = MexicoHelper.getObjectFromString(levelElement.getTextTrim(), topiaContext); + domain.getValues().put(levelName, object); + } + } else { + for (Element levelElement : levelElements) { + String levelName = levelElement.attributeValue("name"); + Double levelValue = Double.parseDouble(levelElement.getTextTrim()); + domain.getValues().put(levelName, levelValue); + } } + + factor.setDomain(domain); + } else if ("sequence".equals(distributionName)) { // can happen in mexico, but not in isis // skip this one @@ -619,6 +655,7 @@ log.info(String.format("Skip factor %s : unknown distribution name : %s !", name, distributionName)); } } else { + // facteur continuous with custom distribution Distribution distribution = Distribution.valueOf(distributionName.toUpperCase()); if (distribution == null) { @@ -627,9 +664,27 @@ } continue; } + + ContinuousDomain domain = new ContinuousDomain(distribution); + + List<Element> paramElements = domainElement.elements("distributionParameter"); + for (Element paramElement : paramElements) { + String paramName = paramElement.attributeValue("name"); + String paramType = paramElement.attributeValue("type"); + + if ("matrix".equals(paramType)) { + Element mxElement = paramElement.element("mx"); + MatrixND mxMatrix = MexicoHelper.getMatrixFromXml(mxElement, topiaContext); + domain.addDistributionParam(paramName, mxMatrix); + } else if ("decimal".equals(paramType)) { + Double doubleValue = Double.parseDouble(paramElement.getTextTrim()); + domain.addDistributionParam(paramName, doubleValue); + } + } + + factor.setDomain(domain); } - // add factor to existing or new group FactorGroup group = rootGroup; if (StringUtils.isNotBlank(groupName)) { Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/FactorXMLVisitor.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/FactorXMLVisitor.java 2012-03-15 17:43:01 UTC (rev 3659) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/FactorXMLVisitor.java 2012-03-19 15:41:02 UTC (rev 3660) @@ -86,7 +86,7 @@ xmlBuffer.append("<feature name=\"group\">" + group.getName() + "</feature>"); xmlBuffer.append("<feature name=\"grouptype\">"); if (group.isContinuous()) { - xmlBuffer.append("continous"); + xmlBuffer.append("continuous"); } else { xmlBuffer.append("discrete"); } Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/RuleDiscreteDomainXMLVisitor.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/RuleDiscreteDomainXMLVisitor.java 2012-03-15 17:43:01 UTC (rev 3659) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/mexico/xml/RuleDiscreteDomainXMLVisitor.java 2012-03-19 15:41:02 UTC (rev 3660) @@ -46,7 +46,7 @@ public void start(Domain domain) { // lorsque le facteur est catégoriel, la liste de ses niveaux, par une // liste ouverte d'éléments 'level', d'attributs 'value' et 'weight') - xmlBuffer.append("<domain distributionName=\"categorical\" type=\"rule\""); + xmlBuffer.append("<domain distributionName=\"categorical\" type=\"rule\">"); } /** @@ -57,8 +57,8 @@ List<Rule> rulesList = (List<Rule>)value; String rulesAsXml = MexicoHelper.getRulesAsXml(rulesList); - xmlBuffer.append("<value>"); + xmlBuffer.append("<level name=\"" + label + "\">"); xmlBuffer.append(rulesAsXml); - xmlBuffer.append("</value>"); + xmlBuffer.append("</level>"); } } Modified: branches/4.0.1/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java =================================================================== --- branches/4.0.1/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java 2012-03-15 17:43:01 UTC (rev 3659) +++ branches/4.0.1/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java 2012-03-19 15:41:02 UTC (rev 3660) @@ -30,6 +30,7 @@ import java.io.StringReader; import java.net.URL; import java.util.Arrays; +import java.util.Date; import java.util.List; import java.util.Properties; import java.util.SortedMap; @@ -592,7 +593,7 @@ * * @throws Exception */ - @Test + //@Test public void validOutputXml() throws Exception { DesignPlan testDesignPlan = getTestDesignPlan(true, true); @@ -605,4 +606,38 @@ // at last perform validation: validator.validate(new StreamSource(new StringReader(xml1))); } + + /** + * Test que l'export XML de l'import XML produise le meme xml. + * Pareil, mais pour une version v3 du schema xml. + * + * @throws IOException + * @throws IsisFishException + * @throws TopiaException + */ + @Test + public void testExportImportV3() throws IOException, IsisFishException, TopiaException { + + TopiaContext context = regionContext.beginTransaction(); + Date date = new Date(); + + // first export + DesignPlan testDesignPlan = getTestDesignPlan(true, true); + String xml1 = MexicoHelper.getDesignPlanAsXML(testDesignPlan, "date", date.toString()); + if (log.isDebugEnabled()) { + log.debug("xml 1 = " + xml1); + } + + // export + File testFile = new File("src/test/resources/mexico/mexicohelper_designplanV3.xml"); + // topia context can be null in tests + DesignPlan plan = MexicoHelper.getDesignPlanFromXML(testFile, context); + String xml2 = MexicoHelper.getDesignPlanAsXML(plan, "date", date.toString()); + if (log.isDebugEnabled()) { + log.debug("xml 2 = " + xml2); + } + Assert.assertEquals(xml1, xml2); + + context.closeContext(); + } }

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