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r2919 - in isis-fish/trunk: . src/main/java/fr/ifremer/isisfish/datastore
by chatellier＠users.labs.libre-entreprise.org Jan. 15, 2010

Jan. 15, 2010

Author: chatellier Date: 2010-01-15 15:45:05 +0000 (Fri, 15 Jan 2010) New Revision: 2919 Modified: isis-fish/trunk/changelog.txt isis-fish/trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java Log: Check if result is enabled by getNecessaryResult on SensitivityExport too Modified: isis-fish/trunk/changelog.txt =================================================================== --- isis-fish/trunk/changelog.txt 2010-01-15 09:41:59 UTC (rev 2918) +++ isis-fish/trunk/changelog.txt 2010-01-15 15:45:05 UTC (rev 2919) @@ -1,5 +1,6 @@ isis-fish (3.3.0.0) stable; urgency=low + * Check if result is enabled by getNecessaryResult on SensitivityExport * Use mexico export format for matrix * Restore simulation tests at integration-test phase * Add region factorisable value export (mexico) Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java 2010-01-15 09:41:59 UTC (rev 2918) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java 2010-01-15 15:45:05 UTC (rev 2919) @@ -1,5 +1,5 @@ /* *##% - * Copyright (C) 2002-2009 + * Copyright (C) 2002-2010 * Ifremer, Code Lutin, Cédric Pineau, Benjamin Poussin * * This program is free software; you can redistribute it and/or @@ -47,6 +47,7 @@ import fr.ifremer.isisfish.entities.Result; import fr.ifremer.isisfish.entities.ResultDAO; import fr.ifremer.isisfish.export.Export; +import fr.ifremer.isisfish.export.SensitivityExport; import fr.ifremer.isisfish.rule.Rule; import fr.ifremer.isisfish.simulator.AnalysePlan; import fr.ifremer.isisfish.simulator.SimulationContext; @@ -187,6 +188,14 @@ * Permet de savoir si lorsque l'on ajoutera ce resultat, il sera * sauvé ou non. * + * Check for result name returned by : + * <ul> + * <li>{@link Export#getNecessaryResult()}</li> + * <li>{@link SensitivityExport#getNecessaryResult()}</li> + * <li>{@link Rule#getNecessaryResult()}</li> + * <li>{@link AnalysePlan#getNecessaryResult()}</li> + * </ul> + * * @param name result name * @return {@code true} if result is enabled */ @@ -197,6 +206,8 @@ Collection<String> resultEnabled = simulation.getParameter().getResultEnabled(); enabledResult.addAll(resultEnabled); + + // test on export List<String> exportNames = simulation.getParameter().getExportNames(); if (exportNames != null) { for (String exportName : exportNames) { @@ -213,6 +224,18 @@ } } } + + // test on sensitivity export + List<SensitivityExport> sensitivityExports = simulation.getParameter().getSensitivityExport(); + if (sensitivityExports != null) { + for (SensitivityExport sensitivityExport : sensitivityExports) { + for (String resultName : sensitivityExport.getNecessaryResult()) { + enabledResult.add(resultName); + } + } + } + + // test on rules List<Rule> rules = simulation.getParameter().getRules(); if (rules != null) { for (Rule rule : rules) { @@ -221,6 +244,8 @@ } } } + + // test on plans List<AnalysePlan> plans = simulation.getParameter().getAnalysePlans(); if (plans != null) { for (AnalysePlan plan : plans) {

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r2918 - isis-fish/trunk
by jcouteau＠users.labs.libre-entreprise.org Jan. 15, 2010

Jan. 15, 2010

Author: jcouteau Date: 2010-01-15 09:41:59 +0000 (Fri, 15 Jan 2010) New Revision: 2918 Modified: isis-fish/trunk/pom.xml Log: Use nuiton utils 1.1.3-SNAPSHOT Modified: isis-fish/trunk/pom.xml =================================================================== --- isis-fish/trunk/pom.xml 2010-01-14 16:06:54 UTC (rev 2917) +++ isis-fish/trunk/pom.xml 2010-01-15 09:41:59 UTC (rev 2918) @@ -434,7 +434,7 @@ <jaxx.version>1.7.1</jaxx.version> <eugene.version>2.0.0-beta-2</eugene.version> <topia.version>2.3.0-beta-3</topia.version> - <nuiton-utils.version>1.1.2</nuiton-utils.version> + <nuiton-utils.version>1.1.3-SNAPSHOT</nuiton-utils.version> <nuiton-i18n.version>1.0.1</nuiton-i18n.version> <nuiton-widgets.version>1.0.1-SNAPSHOT</nuiton-widgets.version> <jrst.version>1.0.0</jrst.version>

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r2917 - isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/input
by chatellier＠users.labs.libre-entreprise.org Jan. 14, 2010

Jan. 14, 2010

Author: chatellier Date: 2010-01-14 16:06:54 +0000 (Thu, 14 Jan 2010) New Revision: 2917 Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/input/InputContentUI.jaxx Log: Disable "next" button. Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/input/InputContentUI.jaxx =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/input/InputContentUI.jaxx 2010-01-14 15:59:19 UTC (rev 2916) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/input/InputContentUI.jaxx 2010-01-14 16:06:54 UTC (rev 2917) @@ -211,5 +211,6 @@ ]]></script> <JPanel id='body' constraints='BorderLayout.CENTER'/> - <JButton id='next' text='{getButtonTitle()}' constraints='BorderLayout.SOUTH' visible='{getNextPath() != null}' onActionPerformed='goTo()'/> + <JButton id='next' text='{getButtonTitle()}' constraints='BorderLayout.SOUTH' + visible='{getNextPath() != null}' onActionPerformed='goTo()' decorator='boxed'/> </JPanel>

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r2916 - isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/simulator
by chatellier＠users.labs.libre-entreprise.org Jan. 14, 2010

Jan. 14, 2010

Author: chatellier Date: 2010-01-14 15:59:19 +0000 (Thu, 14 Jan 2010) New Revision: 2916 Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/SimulAction.java Log: Sort factor on factor name Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/SimulAction.java =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/SimulAction.java 2010-01-14 15:51:55 UTC (rev 2915) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/simulator/SimulAction.java 2010-01-14 15:59:19 UTC (rev 2916) @@ -30,6 +30,8 @@ import java.text.SimpleDateFormat; import java.util.ArrayList; import java.util.Collection; +import java.util.Collections; +import java.util.Comparator; import java.util.HashMap; import java.util.List; import java.util.Map; @@ -809,6 +811,15 @@ for (Map.Entry<?, ?> entry : factors.entrySet()) { result.add((Factor<?, ?>) entry.getValue()); } + + // sort factor on name + Collections.sort(result, new Comparator<Factor<?, ?>> (){ + @Override + public int compare(Factor<?, ?> o1, Factor<?, ?> o2) { + return o1.getName().compareTo(o2.getName()); + } + }); + return result; }

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r2915 - isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity
by chatellier＠users.labs.libre-entreprise.org Jan. 14, 2010

Jan. 14, 2010

Author: chatellier Date: 2010-01-14 15:51:55 +0000 (Thu, 14 Jan 2010) New Revision: 2915 Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/EditorHelper.java Log: RangeOfValues can be continuous. Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/EditorHelper.java =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/EditorHelper.java 2010-01-14 13:28:17 UTC (rev 2914) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/EditorHelper.java 2010-01-14 15:51:55 UTC (rev 2915) @@ -54,6 +54,7 @@ import fr.ifremer.isisfish.simulator.sensitivity.domain.EquationContinuousDomain; import fr.ifremer.isisfish.simulator.sensitivity.domain.MatrixContinuousDomain; import fr.ifremer.isisfish.types.Month; +import fr.ifremer.isisfish.types.RangeOfValues; import fr.ifremer.isisfish.ui.input.InputAction; import fr.ifremer.isisfish.ui.input.InputOneEquationUI; import fr.ifremer.isisfish.ui.input.InputSaveVerifier; @@ -679,6 +680,13 @@ else if (component instanceof MatrixPanelEditor) { result = true; } + // Metier.gearPossibleValue case + else if (value instanceof RangeOfValues) { + RangeOfValues rangeOfValues = (RangeOfValues)value; + if (rangeOfValues.getType().equals("Float")) { + result = true; + } + } if (log.isDebugEnabled()) { log.debug("Component " + component.getClass().getSimpleName() +

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r2914 - isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity
by jcouteau＠users.labs.libre-entreprise.org Jan. 14, 2010

Jan. 14, 2010

Author: jcouteau Date: 2010-01-14 13:28:17 +0000 (Thu, 14 Jan 2010) New Revision: 2914 Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java Log: Fix nominal value for matrices Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java 2010-01-14 08:43:33 UTC (rev 2913) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java 2010-01-14 13:28:17 UTC (rev 2914) @@ -238,6 +238,13 @@ String path = factor.getPath(); String topiaId = path.substring(0,path.lastIndexOf("#")); String propertyName=path.substring(path.lastIndexOf("#") + 1); + + Domain domain =factor.getDomain(); + + if (domain instanceof MatrixContinuousDomain){ + return "1.0"; + } + Object value = null; try { TopiaEntity entity = context.findByTopiaId(topiaId);

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r2913 - isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity
by jcouteau＠users.labs.libre-entreprise.org Jan. 14, 2010

Jan. 14, 2010

Author: jcouteau Date: 2010-01-14 08:43:33 +0000 (Thu, 14 Jan 2010) New Revision: 2913 Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java Log: Improve code Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java 2010-01-13 16:10:41 UTC (rev 2912) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java 2010-01-14 08:43:33 UTC (rev 2913) @@ -21,7 +21,6 @@ import java.io.File; import java.io.IOException; import java.util.Collection; -import java.util.Iterator; import java.util.List; import fr.ifremer.isisfish.datastore.SimulationStorage; @@ -67,7 +66,9 @@ * Method to create the isis.factors dataframe in R. * * @param plan Design plan of the sensitivity analysis - * @param outputdirectory ??? + * @param outputdirectory the directory on which we will calculate the + * destination RData file. The RData file will be named directory.RData and + * saved in the directory parent. * * @throws SensitivityException */ @@ -84,12 +85,7 @@ String binfValues = ""; String bsup = "Bsup<-c(%s)"; String bsupValues = ""; - String attributes = "attributes(isis.factors)<-list(" + - "%s" + - "\"nomModel\"=\"isis-fish-externeR\"," + - "names=c(\"nomFacteur\",\"Nominal\",\"Continu\",\"Binf\",\"Bsup\"))"; String attribute = "attr(isis.factors,\"%s\")<-\"%s\""; - String attributesValues = ""; String isisfactors = "isis.factors<-data.frame(" + "\"nomFacteur\"=nomFacteur," + "\"Nominal\"=Nominal," + @@ -177,7 +173,7 @@ } } - String Rcall = ""; + String Rcall; try { @@ -206,15 +202,13 @@ Rcall = String.format(attribute, "nomModel", "isis-fish-externeR"); engine.voidEval(Rcall); - for (int i = 0; i < factors.size(); i++) { - Factor factor = factors.get(i); + for (Factor factor:factors) { if (factor.getDomain() instanceof DiscreteDomain) { String attributeValues = "list("; Collection values = ((DiscreteDomain) factor.getDomain()) - .getValues().values(); - for (Iterator j = values.iterator(); j.hasNext();) { + .getValues().values(); + for (Object j:values) { attributeValues += j + ","; - j.next(); } attributeValues = attributeValues.substring(0, attributeValues.length() - 1);

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r2912 - isis-fish/trunk
by chatellier＠users.labs.libre-entreprise.org Jan. 13, 2010

Jan. 13, 2010

Author: chatellier Date: 2010-01-13 16:10:41 +0000 (Wed, 13 Jan 2010) New Revision: 2912 Modified: isis-fish/trunk/changelog.txt Log: Update changelog.txt Modified: isis-fish/trunk/changelog.txt =================================================================== --- isis-fish/trunk/changelog.txt 2010-01-13 15:51:55 UTC (rev 2911) +++ isis-fish/trunk/changelog.txt 2010-01-13 16:10:41 UTC (rev 2912) @@ -1,5 +1,6 @@ isis-fish (3.3.0.0) stable; urgency=low + * Use mexico export format for matrix * Restore simulation tests at integration-test phase * Add region factorisable value export (mexico) * Improve simulation stopping algorithm (now faster)

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r2911 - in isis-fish/trunk/src: main/java/fr/ifremer/isisfish/mexico test/java/fr/ifremer/isisfish/mexico
by chatellier＠users.labs.libre-entreprise.org Jan. 13, 2010

Jan. 13, 2010

Author: chatellier Date: 2010-01-13 15:51:55 +0000 (Wed, 13 Jan 2010) New Revision: 2911 Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/mexico/MexicoHelper.java isis-fish/trunk/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java Log: Udpate doc, step attribute not used Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/mexico/MexicoHelper.java =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/mexico/MexicoHelper.java 2010-01-13 15:18:13 UTC (rev 2910) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/mexico/MexicoHelper.java 2010-01-13 15:51:55 UTC (rev 2911) @@ -298,7 +298,7 @@ * * Format is : * <pre> - * <mx step="0" name="une matrice"> + * <mx name="une matrice"> * <dimension name="classe" size="2"> * <label>jeune</label> * <label>vieux</label> @@ -340,17 +340,17 @@ for (Element labelElement : labelElements) { String content = labelElement.getText(); Object value = null; - + if (content != null) { content = content.trim(); - + Pattern matrixPattern = Pattern.compile("^(.*)\$(.*\$)$"); Matcher matcher = matrixPattern.matcher(content); - + if (matcher.find()) { String objectType = matcher.group(1); String objectString = matcher.group(2); - + if (log.isDebugEnabled()) { log.debug("Looking for object : " + objectType + ":" + objectString); } @@ -379,11 +379,11 @@ } semantics.add(semantic); } - + MatrixND result = MatrixFactory.getInstance().create(name, semantics.toArray(new List<?>[semantics.size()]), dimNames.toArray(new String[dimNames.size()])); - + MatrixIterator iterator = result.iterator(); // TODO it's d for double here, can be int... List<Element> values = mxElement.elements("d"); @@ -393,7 +393,7 @@ double doubleValue = Double.parseDouble(text); iterator.setValue(doubleValue); } - + return result; } Modified: isis-fish/trunk/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java =================================================================== --- isis-fish/trunk/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java 2010-01-13 15:18:13 UTC (rev 2910) +++ isis-fish/trunk/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java 2010-01-13 15:51:55 UTC (rev 2911) @@ -149,7 +149,7 @@ // factor 4 Assert.assertTrue(xml.indexOf("<d>-14.0</d>") != -1); Assert.assertTrue(xml.indexOf("0.799") != -1); - Assert.assertTrue(xml.indexOf("<mx name=\"test1\" step=\"0\">") != -1); + Assert.assertTrue(xml.indexOf("<mx name=\"test1\">") != -1); // factor 5 Assert.assertTrue(xml.indexOf("reference=\"45.0\" variable=\"L1\"") != -1);

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r2910 - isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity
by jcouteau＠users.labs.libre-entreprise.org Jan. 13, 2010

Jan. 13, 2010

Author: jcouteau Date: 2010-01-13 15:18:13 +0000 (Wed, 13 Jan 2010) New Revision: 2910 Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java Log: Factorize some code Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java 2010-01-13 14:20:25 UTC (rev 2909) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java 2010-01-13 15:18:13 UTC (rev 2910) @@ -19,13 +19,14 @@ package fr.ifremer.isisfish.simulator.sensitivity; import java.io.File; +import java.io.IOException; import java.util.Collection; import java.util.Iterator; import java.util.List; -import fr.ifremer.isisfish.util.ConverterUtil; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.export.SensitivityExport; import org.apache.commons.beanutils.BeanUtils; -import org.apache.commons.beanutils.ConvertUtilsBean; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.nuiton.j2r.REngine; @@ -38,7 +39,10 @@ import fr.ifremer.isisfish.simulator.sensitivity.domain.MatrixContinuousDomain; import org.nuiton.topia.TopiaContext; import org.nuiton.topia.persistence.TopiaEntity; +import org.nuiton.util.FileUtil; +import javax.swing.*; + public abstract class AbstractSensitivityCalculator implements SensitivityCalculator { @@ -237,7 +241,6 @@ } protected String getNominalValue(Factor factor){ - ConvertUtilsBean beanUtils = ConverterUtil.getConverter(null); String path = factor.getPath(); String topiaId = path.substring(0,path.lastIndexOf("#")); String propertyName=path.substring(path.lastIndexOf("#") + 1); @@ -251,7 +254,98 @@ if (value == null){ return null; } + log.info("Nominal value :" + value); return value.toString(); } + protected String editRInstruction(String rCall){ + JLabel label = new JLabel( + "Modifier le code R envoyé si vous le souhaitez"); + JTextPane text = new JTextPane(); + text.setText(rCall); + text.setSize(400, 400); + text.setPreferredSize(text.getSize()); + + Box box = Box.createVerticalBox(); + box.add(label); + box.add(new JScrollPane(text)); + + JOptionPane.showMessageDialog(null, box, "R modif", + JOptionPane.QUESTION_MESSAGE); + return text.getText(); + } + + protected void testNoDiscrete(List<Factor<?,?>> factors) throws SensitivityException{ + for (Factor factor:factors) { + if (factor.getDomain() instanceof DiscreteDomain) { + throw new SensitivityException(factor.getName() + + " has a discrete domain, this is not acceptable for " + + "this method."); + } + } + } + + protected String createImportInstruction( + SensitivityExport export, + List<SimulationStorage> simulationStorages) { + + //the filename to read + String name = export.getExportFilename(); + //the extension to read + String extension = export.getExtensionFilename(); + //the rInstruction + String rInstruction = name + "<-c("; + + //iterate on all the simulations and read the value for each one + for (int l = 0; l < simulationStorages.size(); l++) { + + SimulationStorage simulationStorage = simulationStorages.get(l); + File directory = simulationStorage.getDirectory(); + + String directoryPath = directory.toString() + File.separator + + SimulationStorage.RESULT_EXPORT_DIRECTORY; + + File importFile = new File(directoryPath, name + extension); + + String simulResult=""; + try{ + simulResult = FileUtil.readAsString(importFile); + } catch (IOException ioe) { + log.error ("An error occured trying to read a result file : " + + ioe.getMessage()); + } + + + double simulationResult = Double.valueOf(simulResult); + + if (l < simulationStorages.size() - 1) { + rInstruction += simulationResult + ","; + } else { + rInstruction += simulationResult; + } + } + rInstruction += ")"; + + return rInstruction; + } + + protected void renameObjects(REngine engine, String simulationName) + throws RException { + + String renameIsisSimule = "%s.isis.simule<-isis.simule"; + String renameIsisFactorDistribution = "%s.isis.factor.distribution" + + "<-isis.factor.distribution"; + String renameIsisFactor = "%s.isis.factor<-isis.factors"; + String renameIsisMethodExp = "%s.isis.methodExp<-isis.MethodExp"; + + engine.voidEval(String.format(renameIsisSimule, simulationName)); + + engine.voidEval(String.format(renameIsisFactorDistribution, + simulationName)); + + engine.voidEval(String.format(renameIsisFactor, simulationName)); + + engine.voidEval(String.format(renameIsisMethodExp, simulationName)); + } + }

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