[Isis-fish-commits] r3334 - in isis-fish/branches/3.3.1/src: main/java/fr/ifremer/isisfish/mexico/xml test/java/fr/ifremer/isisfish/mexico test/resources/mexico

20 May 2011

Author: chatellier
Date: 2011-05-20 15:29:55 +0000 (Fri, 20 May 2011)
New Revision: 3334

Log:
Gestion des types de facteur min/max et pourcentage pour l'import/export xml.

Added:
   isis-fish/branches/3.3.1/src/test/resources/mexico/mexicohelper_designplanV2.xml
Modified:
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/ContinuousDomainXMLVisitor.java
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DesignPlanXMLVisitor.java
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/EquationContinuousDomainXMLVisitor.java
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/FactorXMLVisitor.java
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/MatrixContinuousDomainXMLVisitor.java
   isis-fish/branches/3.3.1/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/ContinuousDomainXMLVisitor.java
===================================================================

--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/ContinuousDomainXMLVisitor.java	2011-05-19 15:30:08 UTC (rev 3333)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/ContinuousDomainXMLVisitor.java	2011-05-20 15:29:55 UTC (rev 3334)
@@ -50,14 +50,28 @@
         ContinuousDomain cDomain = (ContinuousDomain)domain;
         xmlBuffer.append(" cardinality=\"" + cDomain.getCardinality() + "\">");
 
+        appendDomain(cDomain);
+    }
+
+    /**
+     * Default ContinuousDomain implementation for double.
+     * Maybe overridden by specific continuous domains.
+     * 
+     * @param domain domain to print
+     */
+    protected void appendDomain(ContinuousDomain domain) {
         // facteur continue pourcentage
-        if (cDomain.getCoefficient() != null || cDomain.getReferenceValue() != null) {
-            xmlBuffer.append("<percentage coefficient=\"" + cDomain.getCoefficient() + "\"");
-            xmlBuffer.append(" reference=\"" + cDomain.getReferenceValue() + "\" />");
+        if (domain.getCoefficient() != null || domain.getReferenceValue() != null) {
+            xmlBuffer.append("<reference coefficient=\"" + domain.getCoefficient() + "\">");
+            xmlBuffer.append(domain.getReferenceValue());
+            xmlBuffer.append("</reference>");
         }
         else {
             // facteur continue min/max
-            xmlBuffer.append("<range min=\"" + cDomain.getMinBound() + "\" max=\"" + cDomain.getMaxBound() + "\" />");
+            xmlBuffer.append("<range>");
+            xmlBuffer.append("<min>" + domain.getMinBound() + "</min>");
+            xmlBuffer.append("<max>" + domain.getMaxBound() + "</max>");
+            xmlBuffer.append("</range>");
         }
     }
 

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DesignPlanXMLVisitor.java
===================================================================
--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DesignPlanXMLVisitor.java	2011-05-19 15:30:08 UTC (rev 3333)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DesignPlanXMLVisitor.java	2011-05-20 15:29:55 UTC (rev 3334)
@@ -42,10 +42,15 @@
 
     /**
      * {@inheritDoc}
+     * 
+     * Changes :
+     *  v2 : depuis la v2, meilleur gestion des min/max, pourcentage poru quasiment
+     *      tous les facteurs continue
+     *  v0 : version original
      */
     @Override
     public void start(DesignPlan designPlan) {
-        xmlBuffer.append("<experimentalDesign>");
+        xmlBuffer.append("<experimentalDesign version=\"2\">");
     }
 
     /**

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java
===================================================================
--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java	2011-05-19 15:30:08 UTC (rev 3333)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java	2011-05-20 15:29:55 UTC (rev 3334)
@@ -66,10 +66,18 @@
 
         DesignPlan plan = new DesignPlan();
 
+        // could return "2" or null
+        String version = rootElement.attributeValue("version");
+
         List<Element> factorGroupElements = rootElement.selectNodes("child::factors");
         FactorGroup factorGroup = null;
         if (!factorGroupElements.isEmpty()) {
-            factorGroup = parseFactorGroup(factorGroupElements.get(0), topiaContext);
+            if ("2".equals(version)) {
+                factorGroup = parseFactorGroupV2(factorGroupElements.get(0), topiaContext);
+            }
+            else {
+                factorGroup = parseFactorGroup(factorGroupElements.get(0), topiaContext);
+            }
         }
         plan.setFactorGroup(factorGroup);
         
@@ -85,7 +93,12 @@
      * @return factor group
      * 
      * @see FactorGroup#isMixed()
+     * 
+     * @deprecated since 3.4.0.0, this parsing method parse experimentalDesign
+     *      in version "0" or "null" version, don't remove for
+     *      data reading purpose, but could be removed in a future version
      */
+    @Deprecated
     protected static FactorGroup parseFactorGroup(Element fgElement, TopiaContext topiaContext) {
 
         String factorGroupName = fgElement.attributeValue("name");
@@ -266,105 +279,235 @@
 
         return factorGroup;
     }
-
-    /*
-     * Parse element root node as Sensitivity Scenarios.
+    
+    /**
+     * Recursive parse of factor group elements (>factors<).
      * 
-     * @return a {@link SensitivityScenarios}
+     * This version handle xml file with min/max and percentage factor
+     * in each continuous factors.
      * 
-     * TODO : non finished and untested
-     *
-    public static SensitivityScenarios parseSensitivityScenarios(
-            Element rootElement) {
+     * @param fgElement factor group element (>factors<)
+     * @param topiaContext context
+     * @param mixed {@code true} if create factor group need to be mixed
+     * @return factor group
+     * 
+     * @see FactorGroup#isMixed()
+     */
+    protected static FactorGroup parseFactorGroupV2(Element fgElement, TopiaContext topiaContext) {
 
-        SensitivityScenarios scenarios = new SensitivityScenarios();
+        String factorGroupName = fgElement.attributeValue("name");
+        FactorGroup factorGroup = new FactorGroup(factorGroupName);
 
-        List<Element> scenarioElements = rootElement
-                .selectNodes("child::scenarios/scenario");
+        // sub factor group
+        List<Element> factorGroupElements = fgElement.selectNodes("child::factors");
+        for (Element factorGroupElement : factorGroupElements) {
+            FactorGroup subFactorGroup = parseFactorGroupV2(factorGroupElement, topiaContext);
+            factorGroup.addFactor(subFactorGroup);
+        }
+        
+        // normal factors
+        List<Element> factorElements = fgElement.selectNodes("child::factor");
 
-        for (Element scenarioElement : scenarioElements) {
+        for (Element factorElement : factorElements) {
+            String type = factorElement.attributeValue("type");
+            String name = factorElement.attributeValue("name");
+            String property = factorElement.attributeValue("property");
+            String path = factorElement.element("target").getText().trim();
 
-            Scenario scenario = new Scenario();
-            List<Element> factorElements = scenarioElement.elements("factor");
+            // double
+            if ("real".equals(type)) {
+                Factor factor = new Factor(name);
+                factor.setPath(path);
+                Element fixedElement = factorElement.element("domain").element("fixed");
+                // tous les domaines continues
+                if (property.endsWith("continuous")) {
 
-            for (Element factorElement : factorElements) {
-                String type = factorElement.attributeValue("type");
-                String name = factorElement.attributeValue("name");
-                String property = factorElement.attributeValue("property");
-                String path = factorElement.element("target").getText().trim();
+                    ContinuousDomain domain;
+                    if(property.equals("matrixcontinuous")) {
+                        
+                        MatrixContinuousDomain mdomain = new MatrixContinuousDomain();
+                        Element referenceElement = fixedElement.element("reference");
+                        if (referenceElement != null) {
+                            // matrix specific
+                            // <coefficient operator="-" value="0.799"/>
+                            mdomain.setCoefficient(Double.valueOf(referenceElement.attributeValue("coefficient")));
+                            // <mx name="test1" step="0">...
+                            Element matrixElement = referenceElement.element("mx");
+                            MatrixND matrix = MexicoHelper.getMatrixFromXml(matrixElement, topiaContext);
+                            mdomain.setMatrix(matrix);
+                        }
+                        else {
+                            Element rangeElement = fixedElement.element("range");
+                            Element minElement = rangeElement.element("min");
+                            Element maxElement = rangeElement.element("max");
+                            MatrixND minMatrix = MexicoHelper.getMatrixFromXml(minElement.element("mx"), topiaContext);
+                            MatrixND maxMatrix = MexicoHelper.getMatrixFromXml(maxElement.element("mx"), topiaContext);
+                            mdomain.setMinBound(minMatrix);
+                            mdomain.setMaxBound(maxMatrix);
+                        }
 
-                // double
-                if ("real".equals(type)) {
-                    Factor<Double> factor = new Factor<Double>(name);
-                    factor.setPath(path);
-                    factor.setValue(Double.valueOf(factorElement.element(
-                            "value").getText().trim()));
+                        domain = mdomain;
+                    }
+                    else if (property.equals("equationcontinuous")) {
+                        // equation specific
+                        EquationContinuousDomain edomain = new EquationContinuousDomain();
+                        edomain.setVariableName(fixedElement.attributeValue("variable"));
+                        Element referenceElement = fixedElement.element("reference");
+                        if (referenceElement != null) {
+                            edomain.setCoefficient(Double.valueOf(referenceElement.attributeValue("coefficient")));
+                            edomain.setReferenceValue(Double.valueOf(referenceElement.getTextTrim()));
+                        }
+                        else {
+                            Element rangeElement = fixedElement.element("range");
+                            Element minElement = rangeElement.element("min");
+                            Element maxElement = rangeElement.element("max");
+                            edomain.setMinBound(Double.valueOf(minElement.getTextTrim()));
+                            edomain.setMaxBound(Double.valueOf(maxElement.getTextTrim()));
+                        }
 
-                    Element fixedElement = factorElement.element("domain")
-                            .element("fixed");
-                    if ("continuous".equals(property)) {
-                        ContinuousDomain domain = new ContinuousDomain();
-                        domain.setCardinality(Integer.valueOf(fixedElement
-                                .attributeValue("cardinality")));
-                        Element rangeElement = fixedElement.element("range");
-                        domain.setMinBound(Double.valueOf(rangeElement
-                                .attributeValue("min")));
-                        domain.setMaxBound(Double.valueOf(rangeElement
-                                .attributeValue("max")));
-                        factor.setDomain(domain);
-                    } else if ("discrete".equals(property)) {
-                        DiscreteDomain domain = new DiscreteDomain();
-                        List<Element> valueElements = fixedElement.element(
-                                "enumeration").elements("value");
-                        int label = 0;
-                        for (Element valueElement : valueElements) {
-                            domain.getValues().put(
-                                    Integer.valueOf(label),
-                                    Double.valueOf(valueElement.getText()
-                                            .trim()));
-                            ++label;
+                        domain = edomain;
+                    }
+                    else {
+                        // continous domain
+                        domain = new ContinuousDomain();
+
+                        Element referenceElement = fixedElement.element("reference");
+                        if (referenceElement != null) {
+                            domain.setCoefficient(Double.valueOf(referenceElement.attributeValue("coefficient")));
+                            domain.setReferenceValue(Double.valueOf(referenceElement.getTextTrim()));
                         }
-                        factor.setDomain(domain);
+                        else {
+                            // <range max="1.0" min="0.0"/>
+                            Element rangeElement = fixedElement.element("range");
+                            Element minElement = rangeElement.element("min");
+                            Element maxElement = rangeElement.element("max");
+                            domain.setMinBound(Double.valueOf(minElement.getTextTrim()));
+                            domain.setMaxBound(Double.valueOf(maxElement.getTextTrim()));
+                        }
                     }
-                    scenario.getFactors().add(factor);
-                } else if ("integer".equals(type)) {
-                    Factor factor = new Factor(name);
-                    factor.setPath(path);
-                    factor.setValue(Integer.valueOf(factorElement.element(
-                            "value").getText().trim()));
 
-                    Element fixedElement = factorElement.element("domain")
-                            .element("fixed");
-                    if ("continuous".equals(property)) {
-                        ContinuousDomain domain = new ContinuousDomain();
-                        domain.setCardinality(Integer.valueOf(fixedElement
-                                .attributeValue("cardinality")));
-                        Element rangeElement = fixedElement.element("range");
-                        domain.setMinBound(Integer.valueOf(rangeElement
-                                .attributeValue("min")));
-                        domain.setMaxBound(Integer.valueOf(rangeElement
-                                .attributeValue("max")));
-                        factor.setDomain(domain);
-                    } else if ("discrete".equals(property)) {
-                        DiscreteDomain domain = new DiscreteDomain();
-                        List<Element> valueElements = fixedElement.element(
-                                "enumeration").elements("value");
-                        int label = 0;
-                        for (Element valueElement : valueElements) {
-                            domain.getValues().put(
-                                    Integer.valueOf(label),
-                                    Integer.valueOf(valueElement.getText()
-                                            .trim()));
-                            ++label;
+                    domain.setCardinality(Integer.valueOf(fixedElement.attributeValue("cardinality")));
+
+                    factor.setDomain(domain);
+                } else if ("discrete".equals(property)) {
+                    DiscreteDomain domain = new DiscreteDomain();
+                    List<Element> valueElements = fixedElement.element(
+                            "enumeration").elements("value");
+                    int label = 0;
+                    for (Element valueElement : valueElements) {
+                        domain.getValues().put(Integer.valueOf(label),
+                                Double.valueOf(valueElement.getTextTrim()));
+                        ++label;
+                    }
+                    factor.setDomain(domain);
+                }
+                factorGroup.addFactor(factor);
+            } else if ("integer".equals(type)) {
+                Factor factor = new Factor(name);
+                factor.setPath(path);
+                Element fixedElement = factorElement.element("domain").element("fixed");
+                if ("continuous".equals(property)) {
+                    ContinuousDomain domain = null;
+
+                    if(property.equals("matrixcontinuous")) {
+                        
+                        MatrixContinuousDomain mdomain = new MatrixContinuousDomain();
+                        Element referenceElement = fixedElement.element("reference");
+                        if (referenceElement != null) {
+                            // matrix specific
+                            // <coefficient operator="-" value="0.799"/>
+                            mdomain.setCoefficient(Double.valueOf(referenceElement.attributeValue("coefficient")));
+                            // <mx name="test1" step="0">...
+                            Element matrixElement = referenceElement.element("mx");
+                            MatrixND matrix = MexicoHelper.getMatrixFromXml(matrixElement, topiaContext);
+                            mdomain.setMatrix(matrix);
                         }
-                        factor.setDomain(domain);
+                        else {
+                            Element rangeElement = fixedElement.element("range");
+                            Element minElement = rangeElement.element("min");
+                            Element maxElement = rangeElement.element("max");
+                            MatrixND minMatrix = MexicoHelper.getMatrixFromXml(minElement.element("mx"), topiaContext);
+                            MatrixND maxMatrix = MexicoHelper.getMatrixFromXml(maxElement.element("mx"), topiaContext);
+                            mdomain.setMinBound(minMatrix);
+                            mdomain.setMaxBound(maxMatrix);
+                        }
+
+                        domain = mdomain;
                     }
-                    scenario.getFactors().add(factor);
+                    else if (property.equals("equationcontinuous")) {
+                        // equation specific
+                        EquationContinuousDomain edomain = new EquationContinuousDomain();
+                        edomain.setVariableName(fixedElement.attributeValue("variable"));
+                        Element referenceElement = fixedElement.element("reference");
+                        if (referenceElement != null) {
+                            edomain.setCoefficient(Double.valueOf(referenceElement.attributeValue("coefficient")));
+                            edomain.setReferenceValue(Double.valueOf(referenceElement.getTextTrim()));
+                        }
+                        else {
+                            Element rangeElement = fixedElement.element("range");
+                            Element minElement = rangeElement.element("min");
+                            Element maxElement = rangeElement.element("max");
+                            edomain.setMinBound(Double.valueOf(minElement.getTextTrim()));
+                            edomain.setMaxBound(Double.valueOf(maxElement.getTextTrim()));
+                        }
+
+                        domain = edomain;
+                    }
+                    else {
+                        // continous domain
+                        domain = new ContinuousDomain();
+
+                        Element referenceElement = fixedElement.element("reference");
+                        if (referenceElement != null) {
+                            domain.setCoefficient(Double.valueOf(referenceElement.attributeValue("coefficient")));
+                            domain.setReferenceValue(Double.valueOf(referenceElement.getTextTrim()));
+                        }
+                        else {
+                            // <range max="1.0" min="0.0"/>
+                            Element rangeElement = fixedElement.element("range");
+                            Element minElement = rangeElement.element("min");
+                            Element maxElement = rangeElement.element("max");
+                            domain.setMinBound(Integer.valueOf(minElement.getTextTrim()));
+                            domain.setMaxBound(Integer.valueOf(maxElement.getTextTrim()));
+                        }
+                    }
+
+                    domain.setCardinality(Integer.valueOf(fixedElement.attributeValue("cardinality")));
+
+                    factor.setDomain(domain);
+                } else if ("discrete".equals(property)) {
+                    DiscreteDomain domain = new DiscreteDomain();
+                    List<Element> valueElements = fixedElement.element(
+                            "enumeration").elements("value");
+                    int label = 0;
+                    for (Element valueElement : valueElements) {
+                        domain.getValues().put(Integer.valueOf(label),
+                                Integer.valueOf(valueElement.getTextTrim()));
+                        ++label;
+                    }
+                    factor.setDomain(domain);
                 }
+                factorGroup.addFactor(factor);
+            } else if ("rule".equals(type)) {
+                Factor factor = new Factor(name);
+                factor.setPath(path);
+                Element fixedElement = factorElement.element("domain").element("fixed");
+                if ("discrete".equals(property)) {
+                    RuleDomain domain = new RuleDomain();
+                    List<Element> valueElements = fixedElement.element("enumeration").elements("value");
+                    int label = 0;
+                    for (Element valueElement : valueElements) {
+                        Element rulesElement = valueElement.element("rules");
+                        List<Rule> rulesValue = MexicoHelper.getRulesFromXml(rulesElement, topiaContext);
+                        domain.getValues().put(Integer.valueOf(label), rulesValue);
+                        ++label;
+                    }
+                    factor.setDomain(domain);
+                }
+                factorGroup.addFactor(factor);
             }
-            scenarios.getScenarios().add(scenario);
         }
 
-        return scenarios;
-    }*/
+        return factorGroup;
+    }
 }

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/EquationContinuousDomainXMLVisitor.java
===================================================================
--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/EquationContinuousDomainXMLVisitor.java	2011-05-19 15:30:08 UTC (rev 3333)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/EquationContinuousDomainXMLVisitor.java	2011-05-20 15:29:55 UTC (rev 3334)
@@ -26,6 +26,7 @@
 package fr.ifremer.isisfish.mexico.xml;
 
 import fr.ifremer.isisfish.simulator.sensitivity.Domain;
+import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain;
 import fr.ifremer.isisfish.simulator.sensitivity.domain.EquationContinuousDomain;
 
 /**
@@ -44,12 +45,36 @@
      */
     @Override
     public void start(Domain domain) {
-        super.start(domain);
+        xmlBuffer.append("<domain>");
+        xmlBuffer.append("<fixed");
 
         EquationContinuousDomain eDomain = (EquationContinuousDomain)domain;
-        // since 3.3.0.0 coefficient element is outside equation element
-        xmlBuffer.append("<coefficient value=\"" + eDomain.getCoefficient() + "\" />");
-        xmlBuffer.append("<equation variable=\"" + eDomain.getVariableName()+ "\"");
-        xmlBuffer.append(" reference=\"" + eDomain.getReferenceValue() + "\" />");
+        // this version add variable name
+        xmlBuffer.append(" cardinality=\"" + eDomain.getCardinality() + "\" variable=\"" + eDomain.getVariableName()+ "\">");
+
+        appendDomain(eDomain);
     }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    protected void appendDomain(ContinuousDomain domain) {
+
+        EquationContinuousDomain eDomain = (EquationContinuousDomain)domain;
+
+        // facteur continue pourcentage
+        if (domain.getCoefficient() != null || domain.getReferenceValue() != null) {
+            xmlBuffer.append("<reference coefficient=\"" + eDomain.getCoefficient() + "\">");
+            xmlBuffer.append(eDomain.getReferenceValue());
+            xmlBuffer.append("</reference>");
+        }
+        else {
+            // facteur continue min/max
+            xmlBuffer.append("<range>");
+            xmlBuffer.append("<min>" + domain.getOriginalMinBound() + "</min>");
+            xmlBuffer.append("<max>" + domain.getOriginalMaxBound() + "</max>");
+            xmlBuffer.append("</range>");
+        }
+    }
 }

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/FactorXMLVisitor.java
===================================================================
--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/FactorXMLVisitor.java	2011-05-19 15:30:08 UTC (rev 3333)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/FactorXMLVisitor.java	2011-05-20 15:29:55 UTC (rev 3334)
@@ -27,6 +27,8 @@
 
 import java.io.Serializable;
 
+import org.nuiton.math.matrix.MatrixND;
+
 import fr.ifremer.isisfish.rule.Rule;
 import fr.ifremer.isisfish.simulator.sensitivity.Domain;
 import fr.ifremer.isisfish.simulator.sensitivity.Factor;
@@ -59,15 +61,24 @@
         // property attribute
         if (factor.getDomain() instanceof MatrixContinuousDomain) {
             xmlBuffer.append(" property=\"matrixcontinuous\"");
-            referenceValueForType = ((MatrixContinuousDomain)factor.getDomain()).getMinBound();
+            referenceValueForType = ((ContinuousDomain)factor.getDomain()).getReferenceValue();
+            if (referenceValueForType == null) {
+                referenceValueForType = ((ContinuousDomain)factor.getDomain()).getOriginalMinBound();
+            }
         }
         else if (factor.getDomain() instanceof EquationContinuousDomain) {
             xmlBuffer.append(" property=\"equationcontinuous\"");
-            referenceValueForType = ((ContinuousDomain)factor.getDomain()).getMinBound();
+            referenceValueForType = ((ContinuousDomain)factor.getDomain()).getReferenceValue();
+            if (referenceValueForType == null) {
+                referenceValueForType = ((ContinuousDomain)factor.getDomain()).getOriginalMinBound();
+            }
         }
         else if (factor.getDomain() instanceof ContinuousDomain) {
             xmlBuffer.append(" property=\"continuous\"");
-            referenceValueForType = ((ContinuousDomain)factor.getDomain()).getMinBound();
+            referenceValueForType = ((ContinuousDomain)factor.getDomain()).getReferenceValue();
+            if (referenceValueForType == null) {
+                referenceValueForType = ((ContinuousDomain)factor.getDomain()).getOriginalMinBound();
+            }
         }
         else if (factor.getDomain() instanceof DiscreteDomain) {
             xmlBuffer.append(" property=\"discrete\"");
@@ -75,7 +86,8 @@
             referenceValueForType = ((DiscreteDomain)factor.getDomain()).getValues().get(firstKey);
         }
         // type attribute
-        if (referenceValueForType instanceof Double || referenceValueForType instanceof Float) {
+        if (referenceValueForType instanceof Double || referenceValueForType instanceof Float
+                || referenceValueForType instanceof MatrixND) {
             xmlBuffer.append(" type=\"real\"");
         }
         else if (referenceValueForType instanceof Integer) {

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/MatrixContinuousDomainXMLVisitor.java
===================================================================
--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/MatrixContinuousDomainXMLVisitor.java	2011-05-19 15:30:08 UTC (rev 3333)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/MatrixContinuousDomainXMLVisitor.java	2011-05-20 15:29:55 UTC (rev 3334)
@@ -25,8 +25,10 @@
 
 package fr.ifremer.isisfish.mexico.xml;
 
+import org.nuiton.math.matrix.MatrixND;
+
 import fr.ifremer.isisfish.mexico.MexicoHelper;
-import fr.ifremer.isisfish.simulator.sensitivity.Domain;
+import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain;
 import fr.ifremer.isisfish.simulator.sensitivity.domain.MatrixContinuousDomain;
 
 /**
@@ -44,12 +46,22 @@
      * {@inheritDoc}
      */
     @Override
-    public void start(Domain domain) {
-        super.start(domain);
+    protected void appendDomain(ContinuousDomain domain) {
 
         MatrixContinuousDomain mDomain = (MatrixContinuousDomain)domain;
-        // since 3.3.0.0 coefficient element is outside matrix element
-        xmlBuffer.append("<coefficient value=\"" + mDomain.getCoefficient() + "\" />");
-        xmlBuffer.append(MexicoHelper.getMatrixAsXML(mDomain.getMatrix()));
+
+        // facteur continue pourcentage
+        if (domain.getCoefficient() != null || domain.getReferenceValue() != null) {
+            xmlBuffer.append("<reference coefficient=\"" + mDomain.getCoefficient() + "\">");
+            xmlBuffer.append(MexicoHelper.getMatrixAsXML(mDomain.getMatrix()));
+            xmlBuffer.append("</reference>");
+        }
+        else {
+            // facteur continue min/max
+            xmlBuffer.append("<range>");
+            xmlBuffer.append("<min>" + MexicoHelper.getMatrixAsXML((MatrixND)mDomain.getOriginalMaxBound()) + "</min>");
+            xmlBuffer.append("<max>" + MexicoHelper.getMatrixAsXML((MatrixND)mDomain.getOriginalMaxBound()) + "</max>");
+            xmlBuffer.append("</range>");
+        }
     }
 }

Modified: isis-fish/branches/3.3.1/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java
===================================================================
--- isis-fish/branches/3.3.1/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java	2011-05-19 15:30:08 UTC (rev 3333)
+++ isis-fish/branches/3.3.1/src/test/java/fr/ifremer/isisfish/mexico/MexicoHelperTest.java	2011-05-20 15:29:55 UTC (rev 3334)
@@ -33,12 +33,14 @@
 import java.util.SortedMap;
 import java.util.TreeMap;
 
+import org.apache.commons.io.FileUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
 import org.nuiton.math.matrix.MatrixFactory;
+import org.nuiton.math.matrix.MatrixHelper;
 import org.nuiton.math.matrix.MatrixND;
 import org.nuiton.topia.TopiaContext;
 
@@ -222,18 +224,20 @@
         String xml = MexicoHelper.getDesignPlanAsXML(testDesignPlan);
 
         // factor 1
-        Assert.assertTrue(xml.indexOf("<range min=\"0.0\" max=\"50.0\"/>") != -1);
+        Assert.assertTrue(xml.contains("<min>0.0</min>"));
+        Assert.assertTrue(xml.contains("<max>50.0</max>"));
         // factor 2
-        Assert.assertTrue(xml.indexOf("<factor name=\"factor 2 (double discrete)\"") != -1);
-        Assert.assertTrue(xml.indexOf("<value>70.9</value>") != -1);
+        Assert.assertTrue(xml.contains("<factor name=\"factor 2 (double discrete)\""));
+        Assert.assertTrue(xml.contains("<value>70.9</value>"));
         // factor 3
-        Assert.assertTrue(xml.indexOf("<value>14</value>") != -1);
+        Assert.assertTrue(xml.contains("<value>14</value>"));
         // 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\">") != -1);
+        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.indexOf("variable=\"L1\" reference=\"45.0\"") != -1);
+        Assert.assertTrue(xml.contains("<fixed cardinality=\"0\" variable=\"L1\">"));
+        Assert.assertTrue(xml.contains("<reference coefficient=\"0.1\">45.0</reference>"));
 
         if (log.isDebugEnabled()) {
             log.debug("testGetDesignPlanAsXML xml = " + xml);
@@ -352,4 +356,91 @@
         }
         Assert.assertEquals(xml1, xml2);
     }
+
+    /**
+     * Test l'ajout des nouveaux type de facteurs, min/max et pourcentage.
+     * 
+     * @throws IOException
+     * @throws IsisFishException
+     */
+    @Test
+    public void testPercentageMinMaxFactor() throws IOException, IsisFishException {
+
+        // get test plan and add some STRANGES factors
+        DesignPlan testDesignPlan = getTestDesignPlan(false);
+        
+        // matrix 1
+        MatrixND matrix1 = MatrixFactory.getInstance().create("test1",
+                new int[] { 3, 2 }, new String[] { "col1", "col2" });
+        matrix1 = MatrixHelper.convertToId(matrix1);
+        
+        // factor x1
+        Factor factorContinuous = new Factor("factor x1");
+        ContinuousDomain domain1 = new ContinuousDomain();
+        domain1.setReferenceValue(42.0);
+        domain1.setCoefficient(0.05);
+        factorContinuous.setDomain(domain1);
+        factorContinuous.setPath("fr.ifremer.isisfish.entities.PopulationGroup#1156461521013#0.1715620681984218#maxLength");
+
+        // factor x4
+        Factor factorMatrixContinuous = new Factor("factor x4");
+        MatrixContinuousDomain domain4 = new MatrixContinuousDomain();
+        domain4.setMinBound(matrix1);
+        domain4.setMaxBound(matrix1);
+        factorMatrixContinuous.setDomain(domain4);
+        factorMatrixContinuous.setPath("fr.ifremer.isisfish.entities.PopulationGroup#1156461521076#0.6526656643346673#minLength");
+
+        // factor x5
+        Factor factorEquationContinuous = new Factor("factor x5");
+        EquationContinuousDomain domain5 = new EquationContinuousDomain();
+        domain5.setMinBound(40.0);
+        domain5.setMaxBound(50.0);
+        domain5.setVariableName("Lx1");
+        factorEquationContinuous.setDomain(domain5);
+        factorEquationContinuous.setPath("fr.ifremer.isisfish.entities.PopulationGroup#1156461521076#0.6526656643346673#maxLength");
+        
+        testDesignPlan.addFactor(factorContinuous);
+        testDesignPlan.addFactor(factorMatrixContinuous);
+        testDesignPlan.addFactor(factorEquationContinuous);
+        
+        // test write
+        String content = MexicoHelper.getDesignPlanAsXML(testDesignPlan);
+        File tempFile = File.createTempFile("testdesignplan", ".xml");
+        tempFile.deleteOnExit();
+        FileUtils.writeStringToFile(tempFile, content);
+        
+        // test to read it and get content
+        DesignPlan plan = MexicoHelper.getDesignPlanFromXML(tempFile, null);
+        String reReadContent = MexicoHelper.getDesignPlanAsXML(plan);
+
+        Assert.assertEquals(content, reReadContent);
+    }
+    
+    /**
+     * Test que l'export XML de l'import XML produise le meme xml.
+     * Pareil, mais pour une version v2 du schema xml.
+     * 
+     * @throws IOException
+     * @throws IsisFishException 
+     */
+    @Test
+    public void testExportImportV2() throws IOException, IsisFishException {
+
+        // first export
+        DesignPlan testDesignPlan = getTestDesignPlan(false);
+        String xml1 = MexicoHelper.getDesignPlanAsXML(testDesignPlan);
+        if (log.isDebugEnabled()) {
+            log.debug("xml 1 = " + xml1);
+        }
+
+        // export
+        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);
+        if (log.isDebugEnabled()) {
+            log.debug("xml 2 = " + xml2);
+        }
+        Assert.assertEquals(xml1, xml2);
+    }
 }

Added: isis-fish/branches/3.3.1/src/test/resources/mexico/mexicohelper_designplanV2.xml
===================================================================
--- isis-fish/branches/3.3.1/src/test/resources/mexico/mexicohelper_designplanV2.xml	                        (rev 0)
+++ isis-fish/branches/3.3.1/src/test/resources/mexico/mexicohelper_designplanV2.xml	2011-05-20 15:29:55 UTC (rev 3334)
@@ -0,0 +1,84 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<experimentalDesign version="2">
+  <factors>
+    <factor name="factor 1 (double continuous)" property="continuous" type="real">
+      <target>fr.ifremer.isisfish.entities.PopulationGroup#1156461521013#0.1715620681984218#maxLength</target>
+      <domain>
+        <fixed cardinality="0">
+          <range>
+            <min>0.0</min>
+            <max>50.0</max>
+          </range>
+        </fixed>
+      </domain>
+    </factor>
+    <factor name="factor 2 (double discrete)" property="discrete" type="real">
+      <target>fr.ifremer.isisfish.entities.PopulationGroup#1156461521064#0.022976136053553198#minLength</target>
+      <domain>
+        <fixed cardinality="5">
+          <enumeration>
+            <value>12.3</value>
+            <value>70.9</value>
+            <value>21.0</value>
+            <value>-12.1</value>
+            <value>-8.45</value>
+          </enumeration>
+        </fixed>
+      </domain>
+    </factor>
+    <factor name="factor 3 (integer discrete)" property="discrete" type="integer">
+      <target>fr.ifremer.isisfish.entities.PopulationGroup#1156461521076#0.6526656643346673#minLength</target>
+      <domain>
+        <fixed cardinality="3">
+          <enumeration>
+            <value>13</value>
+            <value>14</value>
+            <value>45</value>
+          </enumeration>
+        </fixed>
+      </domain>
+    </factor>
+    <factor name="factor 4 (MatrixContinuous)" property="matrixcontinuous" type="real">
+      <target>fr.ifremer.isisfish.entities.PopulationGroup#1156461521076#0.6526656643346673#minLength</target>
+      <domain>
+        <fixed cardinality="0">
+          <reference coefficient="0.799">
+            <mx name="test1">
+              <dimension name="col1" size="3">
+                <label>null()</label>
+                <label>null()</label>
+                <label>null()</label>
+              </dimension>
+              <dimension name="col2" size="2">
+                <label>null()</label>
+                <label>null()</label>
+              </dimension>
+              <d>13.0</d>
+              <d>-14.0</d>
+              <d>21.0</d>
+              <d>2.0</d>
+              <d>12.0</d>
+              <d>-1.0</d>
+            </mx>
+          </reference>
+        </fixed>
+      </domain>
+    </factor>
+    <factor name="factor 5 (EquationContinuous)" property="equationcontinuous" type="real">
+      <target>fr.ifremer.isisfish.entities.PopulationGroup#1156461521076#0.6526656643346673#maxLength</target>
+      <domain>
+        <fixed cardinality="0" variable="L1">
+          <reference coefficient="0.1">45.0</reference>
+        </fixed>
+      </domain>
+    </factor>
+    <factor name="factor 6 (double continuous percentage)" property="continuous" type="real">
+      <target>fr.ifremer.isisfish.entities.PopulationGroup#1142003453434#0.223499349929004#size</target>
+      <domain>
+        <fixed cardinality="5">
+          <reference coefficient="5.0">14.0</reference>
+        </fixed>
+      </domain>
+    </factor>
+  </factors>
+</experimentalDesign>

    

[Isis-fish-commits] r3334 - in isis-fish/branches/3.3.1/src: main/java/fr/ifremer/isisfish/mexico/xml test/java/fr/ifremer/isisfish/mexico test/resources/mexico

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