Changeset 6473

Timestamp:

Jun 11, 2014, 3:48:39 PM (8 years ago)

Author:

Nicklas Nordborg

Message:

References #1809: Upgrade 3-rd party libraries

Updated JDOM to 2.0.5. This is a not a plug-in replacement for JDOM 1.1. Since we expose some JDOM 1.1 classes in XMLUtil and other classes, we will ship both JDOM versions in BASE 3.4. All places which use JDOM 1.1 have been deprecated and they will be removed in BASE 3.5.

Location:

trunk

Files:

• .classpath (modified) (2 diffs)
• doc/3rd-party-components.txt (modified) (1 diff)
• lib/dist/jaxen-1.1.1.jar (deleted)
• lib/dist/jaxen-1.1.6.jar (added)
• lib/dist/jdom-2.0.5.jar (added)
• src/clients/web/net/sf/basedb/clients/web/extensions/ServletLoader.java (modified) (5 diffs)
• src/clients/web/net/sf/basedb/clients/web/plugins/XMLTemplate.java (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/servlet/RssNewsFeed.java (modified) (1 diff)
• src/core/net/sf/basedb/core/ExtendedProperties.java (modified) (7 diffs)
• src/core/net/sf/basedb/core/HibernateUtil.java (modified) (5 diffs)
• src/core/net/sf/basedb/core/Install.java (modified) (8 diffs)
• src/core/net/sf/basedb/core/PluginConfiguration.java (modified) (6 diffs)
• src/core/net/sf/basedb/core/PredefinedQuery.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/Presets.java (modified) (7 diffs)
• src/core/net/sf/basedb/core/RawDataTypes.java (modified) (10 diffs)
• src/core/net/sf/basedb/util/XMLUtil.java (modified) (1 diff)
• src/core/net/sf/basedb/util/extensions/manager/processor/PluginInstallationProcessor.java (modified) (4 diffs)
• src/core/net/sf/basedb/util/extensions/xml/ExtensionPointFilter.java (modified) (1 diff)
• src/core/net/sf/basedb/util/extensions/xml/PluginDefinitionFilter.java (modified) (1 diff)
• src/core/net/sf/basedb/util/extensions/xml/XmlLoader.java (modified) (11 diffs)
• src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java (modified) (10 diffs)
• src/plugins/core/net/sf/basedb/plugins/HelpExporter.java (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/HelpImporter.java (modified) (4 diffs)
• src/plugins/core/net/sf/basedb/plugins/PluginConfigurationExporter.java (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/PluginConfigurationImporter.java (modified) (6 diffs)
• src/plugins/core/net/sf/basedb/plugins/executor/ParameterDefinition.java (modified) (6 diffs)
• src/test/TestXMLUtil.java (modified) (3 diffs)
• src/test/data/JarPluginManifest.txt (modified) (1 diff)

trunk/.classpath

@@ -23 +23 @@
   <classpathentry kind="lib" path="lib/dist/httpcore-4.2.3.jar"/>
   <classpathentry kind="lib" path="lib/dist/jcommon-1.0.17.jar"/>
-  <classpathentry kind="lib" path="lib/dist/jdom-1.1.3.jar"/>
   <classpathentry kind="lib" path="lib/dist/jfreechart-1.0.14.jar"/>
   <classpathentry kind="lib" path="lib/dist/json-simple-1.1.1.jar"/>
@@ -32 +31 @@
   <classpathentry kind="lib" path="lib/dist/hibernate-core-4.3.5.Final.jar"/>
   <classpathentry kind="lib" path="lib/dist/postgresql-9.3-1101.jdbc41.jar"/>
+  <classpathentry kind="lib" path="lib/dist/jdom-2.0.5.jar"/>
+  <classpathentry kind="lib" path="lib/dist/jdom-1.1.3.jar"/>
   <classpathentry kind="output" path="xbin"/>
 </classpath>

trunk/doc/3rd-party-components.txt

@@ -79 +79 @@
 
 More info : http://www.jdom.org/
-Version   : 1.1.3
+Version   : 2.0.5 and 1.1.3 (deprecated)
 License   : Apache-style open source license (jdom.license.txt)
-Jar files : jdom-1.1.3.jar, jaxen-1.1.1.jar
+Jar files : jdom-2.0.5.jar, jdom-1.1.3.jar, jaxen-1.1.6.jar
 
 

trunk/src/clients/web/net/sf/basedb/clients/web/extensions/ServletLoader.java

@@ -31 +31 @@
 import net.sf.basedb.util.ClassUtil;
 import net.sf.basedb.util.Values;
-import net.sf.basedb.util.XMLUtil;
+import net.sf.basedb.util.XmlUtil2;
 import net.sf.basedb.util.extensions.xml.XmlLoader;
 
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.Namespace;
+import org.jdom2.Document;
+import org.jdom2.Element;
+import org.jdom2.JDOMException;
+import org.jdom2.Namespace;
 
 /**
@@ -107 +107 @@
   public void loadXmlFile(InputStream xmlFile, String filename,
       ClassLoader classLoader, boolean clear)
-    throws JDOMException, IOException, ClassNotFoundException, NoSuchMethodException,
+    throws IOException, ClassNotFoundException, NoSuchMethodException,
       IllegalAccessException
   {
@@ -126 +126 @@
   */
   public void validateXmlFile(InputStream xmlFile, String filename)
-    throws IOException, JDOMException
+    throws IOException
   {
     validatedDom = null;
@@ -195 +195 @@
   */
   protected Document loadDocument(InputStream xmlFile, String filename)
-    throws IOException, JDOMException
-  {
-    return XMLUtil.getSchemaValidatedXML(xmlFile, filename, namespace, schemaFileURL);
+    throws IOException
+  {
+    return XmlUtil2.getSchemaValidatedXML(xmlFile, filename, namespace, schemaFileURL);
   }
   
@@ -203 +203 @@
     Load the servlet definitions from an XML document.
   */
-  @SuppressWarnings("unchecked")
   protected int loadServlets(Document dom, ClassLoader classLoader)
     throws ClassNotFoundException, NoSuchMethodException, IllegalAccessException

trunk/src/clients/web/net/sf/basedb/clients/web/plugins/XMLTemplate.java

@@ -30 +30 @@
 import net.sf.basedb.core.Item;
 
-import org.jdom.DocType;
-import org.jdom.Element;
-import org.jdom.output.Format;
-import org.jdom.output.XMLOutputter;
+import org.jdom2.DocType;
+import org.jdom2.Element;
+import org.jdom2.output.Format;
+import org.jdom2.output.XMLOutputter;
 
 /**

trunk/src/clients/web/net/sf/basedb/clients/web/servlet/RssNewsFeed.java

@@ -35 +35 @@
 import javax.servlet.http.HttpServletResponse;
 
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.output.Format;
-import org.jdom.output.XMLOutputter;
+import org.jdom2.Document;
+import org.jdom2.Element;
+import org.jdom2.output.Format;
+import org.jdom2.output.XMLOutputter;
 
 import net.sf.basedb.core.Application;

trunk/src/core/net/sf/basedb/core/ExtendedProperties.java

@@ -26 +26 @@
 import net.sf.basedb.core.dbengine.DbEngine;
 import net.sf.basedb.util.Values;
-import net.sf.basedb.util.XMLUtil;
+import net.sf.basedb.util.XmlUtil2;
 
 import java.util.HashSet;
@@ -37 +37 @@
 import java.net.URL;
 
-import org.jdom.Document;
-import org.jdom.Element;
+import org.jdom2.Document;
+import org.jdom2.Element;
 
 /**
@@ -120 +120 @@
       {
         log.debug("Loading extended properties from file: " + xmlFile);
-        Document dom = XMLUtil.getValidatedXml(ExtendedProperties.class.getResource(xmlFile), dtdFile);
+        Document dom = XmlUtil2.getValidatedXml(ExtendedProperties.class.getResource(xmlFile), dtdFile);
         loadClasses(usedNames, dom, xmlFile);
         log.info("Loaded extended properties from file: " + xmlFile);
@@ -200 +200 @@
     variable.
   */
-  @SuppressWarnings("unchecked")
   private static void loadClasses(Set<String> usedNames, Document dom, String xmlFile)
   {
-    List<Element> classTags = (List<Element>)dom.getRootElement().getChildren("class");
+    List<Element> classTags = dom.getRootElement().getChildren("class");
     for (Element el : classTags)
     {
@@ -220 +219 @@
     put the list in the {@link #allProperties} variable.
   */
-  @SuppressWarnings("unchecked")
   private static void loadProperties(Set<String> usedNames, Element classElement, String xmlFile)
   {
     String className = classElement.getAttributeValue("name");
     List<ExtendedProperty> properties = allProperties.get(className);
-    List<Element> children = (List<Element>)classElement.getChildren("property");
+    List<Element> children = classElement.getChildren("property");
     DbEngine engine = HibernateUtil.getDbEngine();
     for (Element property : children)
@@ -258 +256 @@
       usedNames.add(idColumn);
       String description = Values.getStringOrNull(property.getAttributeValue("description"));
-      int length = XMLUtil.getIntAttribute(property, "length", 255);
+      int length = XmlUtil2.getIntAttribute(property, "length", 255);
       Type type = Type.fromValue(property.getAttributeValue("type"));
       if (type == Type.STRING && length > 255) type = Type.TEXT;
-      boolean nullable = XMLUtil.getBooleanAttribute(property, "null", true);
-      boolean insertable = XMLUtil.getBooleanAttribute(property, "insert", true);
-      boolean updateable = XMLUtil.getBooleanAttribute(property, "update", true);
-      boolean restrictedEdit = XMLUtil.getBooleanAttribute(property, "restricted-edit", false);
+      boolean nullable = XmlUtil2.getBooleanAttribute(property, "null", true);
+      boolean insertable = XmlUtil2.getBooleanAttribute(property, "insert", true);
+      boolean updateable = XmlUtil2.getBooleanAttribute(property, "update", true);
+      boolean restrictedEdit = XmlUtil2.getBooleanAttribute(property, "restricted-edit", false);
       String avgMethod = property.getAttributeValue("averagemethod");
       Formula.AverageMethod averageMethod = null;
@@ -280 +278 @@
       }
       
-      List<Element> links = (List<Element>)property.getChildren("link");
+      List<Element> links = property.getChildren("link");
       List<ExtendedPropertyLinker> epLinks = null;
       if (links != null && links.size() > 0)

trunk/src/core/net/sf/basedb/core/HibernateUtil.java

@@ -50 +50 @@
 import net.sf.basedb.util.FileUtil;
 import net.sf.basedb.util.RegexpFileFilter;
-import net.sf.basedb.util.XMLUtil;
+import net.sf.basedb.util.XmlUtil2;
 
 import java.util.ArrayList;
@@ -68 +68 @@
 import java.net.URL;
 
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.output.DOMOutputter;
+import org.jdom2.Document;
+import org.jdom2.Element;
+import org.jdom2.output.DOMOutputter;
 import org.hibernate.Hibernate;
 import org.hibernate.Interceptor;
@@ -307 +307 @@
       {
         log.info("Loading mapping file: " + url);
-        Document dom = XMLUtil.getValidatedXml(url, dtdFile);
+        Document dom = XmlUtil2.getValidatedXml(url, dtdFile);
         manipulateDocument(dom);
         cfg.addDocument(out.output(dom));
@@ -513 +513 @@
         try
         {
-          Document dom = XMLUtil.getValidatedXml(templateFile, dtdFile);
+          Document dom = XmlUtil2.getValidatedXml(templateFile, dtdFile);
           Element clazz = dom.getRootElement().getChild("class");
           // Specify an entity name and database table for the raw data type
@@ -581 +581 @@
     
     // Find the class/property/column[name=`symbol`] tag
-    Iterator match = classTag.getDescendants(
-      new org.jdom.filter.Filter()
+    Iterator<Element> match = classTag.getDescendants(
+      new org.jdom2.filter.AbstractFilter<Element>()
       {
         private static final long serialVersionUID = -2876632679035736428L;
         @Override
-        public boolean matches(Object obj)
+        public Element filter(Object obj)
         {
-          if (!(obj instanceof Element)) return false;
+          if (!(obj instanceof Element)) return null;
   
           Element e = (Element)obj;
-          return e.getName().equals("column") && e.getAttributeValue("name").equals("`symbol`");
+          return e.getName().equals("column") && e.getAttributeValue("name").equals("`symbol`") ? e : null;
         }
       });
     Element col = (Element)match.next();
-    String sqlType = dbEngine.getCaseSensitiveVarchar(XMLUtil.getIntAttribute(col, "length", 255));
+    String sqlType = dbEngine.getCaseSensitiveVarchar(XmlUtil2.getIntAttribute(col, "length", 255));
     if (sqlType != null) 
     {

trunk/src/core/net/sf/basedb/core/Install.java

@@ -69 +69 @@
 import net.sf.basedb.util.FileUtil;
 import net.sf.basedb.util.Values;
-import net.sf.basedb.util.XMLUtil;
+import net.sf.basedb.util.XmlUtil2;
 import net.sf.basedb.util.extensions.manager.Settings;
 import net.sf.basedb.util.extensions.xml.PluginInfo;
@@ -86 +86 @@
 import java.util.Set;
 
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.Namespace;
+import org.jdom2.Document;
+import org.jdom2.Element;
+import org.jdom2.Namespace;
 
 /**
@@ -1392 +1392 @@
   }
   
-  @SuppressWarnings("unchecked")
   private static void installUnits(String xmlFile, boolean update)
   {
@@ -1402 +1401 @@
     try
     {
-      doc = XMLUtil.getSchemaValidatedXML(fileURL, namespace, schemaFileURL);
+      doc = XmlUtil2.getSchemaValidatedXML(fileURL, namespace, schemaFileURL);
     }
     catch (Exception ex)
@@ -1413 +1412 @@
     Namespace ns = root.getNamespace();
     
-    for (Element quantityElement : (List<Element>)root.getChildren("quantity", ns))
+    for (Element quantityElement : root.getChildren("quantity", ns))
     {
       String systemId = quantityElement.getAttributeValue("system-id");
@@ -2459 +2458 @@
     Create {@link PluginConfiguration}s from a XML file.
   */
-  @SuppressWarnings("unchecked")
   private static void createPluginConfigurations(String filePath, boolean update)
     throws BaseException
@@ -2484 +2482 @@
       }
       
-      List<Element> configurations = PluginConfiguration.loadXmlFile(Install.class.getResource(filePath).openStream(), filePath);
+      List<Element> configurations = PluginConfiguration.loadXmlFile2(Install.class.getResource(filePath).openStream(), filePath);
       
       for (Element configuration : configurations)
@@ -2520 +2518 @@
           config.setName(name);
           config.setDescription(description);
-          config.setParameterValues((List<Element>)configuration.getChildren("parameter"));
+          config.setParameterValues2((List<Element>)configuration.getChildren("parameter"));
         }       
         catch(Throwable ex)

trunk/src/core/net/sf/basedb/core/PluginConfiguration.java

@@ -35 +35 @@
 import net.sf.basedb.core.query.Hql;
 import net.sf.basedb.core.query.Expressions;
-import net.sf.basedb.util.XMLUtil;
+import net.sf.basedb.util.XmlUtil2;
 
 import java.io.IOException;
@@ -48 +48 @@
 import java.util.Collections;
 
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
+import org.jdom2.Document;
+import org.jdom2.Element;
+//import org.jdom2.JDOMException;
 
 /**
@@ -182 +182 @@
     @return A list with all <configuration> elements in the file
     @since 3.0
+    @deprecated In 3.4, use {@link #loadXmlFile2(InputStream, String)} instead
   */
   @SuppressWarnings("unchecked")
-  public static List<Element> loadXmlFile(InputStream in, String fileName)
-    throws IOException, JDOMException
+  @Deprecated
+  public static List<org.jdom.Element> loadXmlFile(InputStream in, String fileName)
+    throws IOException, org.jdom.JDOMException
   {
     URL dtdURL = PluginConfiguration.class.getResource("/net/sf/basedb/core/dtd/plugin-configuration-file.dtd");
-    Document doc = XMLUtil.getValidatedXML(in, dtdURL, fileName);
+    org.jdom.Document doc = net.sf.basedb.util.XMLUtil.getValidatedXML(in, dtdURL, fileName);
+    org.jdom.Element rootElement = doc.getRootElement();
+    return (List<org.jdom.Element>)rootElement.getChildren();
+  }
+  
+  /**
+    Load a configurations xml file from the given stream.
+    @param in The input stream to read from
+    @param fileName The name of the originating file (optional)
+    @return A list with all &lt;configuration&gt; elements in the file
+    @since 3.4
+  */
+  public static List<Element> loadXmlFile2(InputStream in, String fileName)
+    throws IOException
+  {
+    URL dtdURL = PluginConfiguration.class.getResource("/net/sf/basedb/core/dtd/plugin-configuration-file.dtd");
+    Document doc = XmlUtil2.getValidatedXML(in, dtdURL, fileName);
     Element rootElement = doc.getRootElement();
     return (List<Element>)rootElement.getChildren();
@@ -706 +724 @@
       @throws ClassNotFoundException If there is an error while trying to find the type of the parameters.
       @since 3.0
+      @deprecated In 3.4, use {@link #setParameterValues2} instead
   */
   @SuppressWarnings("unchecked")
-  public void setParameterValues(List<Element> parameters)
+  @Deprecated
+  public void setParameterValues(List<org.jdom.Element> parameters)
     throws ClassNotFoundException
   {
     checkPermission(Permission.WRITE);
     // Set each configuration parameter for the plugin.
-    for (Element parameter : parameters)
+    for (org.jdom.Element parameter : parameters)
     { 
       String name = parameter.getChildText("name");               
@@ -734 +754 @@
   
   /**
+    Sets parameters for a PluginConfiguration from the elements in a xml
+    configurations file.
+    
+      @param parameters A list of the parameters that shall be set to the configuration
+      @throws ClassNotFoundException If there is an error while trying to find the type of the parameters.
+      @since 3.4
+  */
+  @SuppressWarnings("unchecked")
+  public void setParameterValues2(List<Element> parameters)
+    throws ClassNotFoundException
+  {
+    checkPermission(Permission.WRITE);
+    // Set each configuration parameter for the plugin.
+    for (Element parameter : parameters)
+    { 
+      String name = parameter.getChildText("name");               
+      String cl = parameter.getChildText("class"); 
+      String label = parameter.getChildText("label");
+      if (label == null || label.length() == 0) label = name;   
+      String description = parameter.getChildText("description");
+      Class clazz = null;
+      List values = null;
+      
+      if (cl.length() > 0)
+      {
+        clazz = Class.forName(cl);
+        values = getValueList2(parameter, clazz);
+        ParameterType pType = getParameterType(clazz, values);
+        setParameterValues(name,label, description, pType, values);
+      }
+    }
+  }
+
+  
+  /**
       Gets the list of values for a parameter from the XML-file.
       Returns a list with parameter values.
   */  
   @SuppressWarnings("unchecked")
-  private <T> List<T> getValueList(Element parameter, Class<T> classType)
+  @Deprecated
+  private <T> List<T> getValueList(org.jdom.Element parameter, Class<T> classType)
   { 
-    List<Element> children = (List<Element>)parameter.getChildren("value");
+    List<org.jdom.Element> children = (List<org.jdom.Element>)parameter.getChildren("value");
     List<T> values = new ArrayList<T>();
-    for (Object ch : children)
-    {
-      String text = ((Element)ch).getText();
+    for (org.jdom.Element ch : children)
+    {
+      String text = ch.getText();
       if (classType.equals(Boolean.class)) values.add((T)Boolean.valueOf(text));
       else if (classType.equals(Date.class)) values.add((T)DateUtil.parseString(text));
@@ -755 +811 @@
   }
   
+  /**
+      Gets the list of values for a parameter from the XML-file.
+      Returns a list with parameter values.
+  */
+  @SuppressWarnings("unchecked")
+  private <T> List<T> getValueList2(Element parameter, Class<T> classType)
+  { 
+    List<Element> children = parameter.getChildren("value");
+    List<T> values = new ArrayList<T>();
+    for (Element ch : children)
+    {
+      String text = ch.getText();
+      if (classType.equals(Boolean.class)) values.add((T)Boolean.valueOf(text));
+      else if (classType.equals(Date.class)) values.add((T)DateUtil.parseString(text));
+      else if (classType.equals(Double.class)) values.add((T)Double.valueOf(text));
+      else if (classType.equals(Float.class)) values.add((T)Float.valueOf(text));
+      else if (classType.equals(Long.class)) values.add((T)Long.valueOf(text));
+      else if (classType.equals(String.class)) values.add((T)text);
+    }
+    return values;
+  }
+
   /**
       Gets the ParameterType to use with a class.

trunk/src/core/net/sf/basedb/core/PredefinedQuery.java

@@ -23 +23 @@
 package net.sf.basedb.core;
 
-import net.sf.basedb.util.XMLUtil;
+import net.sf.basedb.util.XmlUtil2;
 
 import java.net.URL;
 import java.util.Arrays;
 
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.xpath.XPath;
+import org.jdom2.Document;
+import org.jdom2.Element;
+import org.jdom2.xpath.XPathExpression;
+import org.jdom2.xpath.XPathFactory;
 
 /**
@@ -106 +106 @@
     try
     {
-      commonDom = XMLUtil.getValidatedXml(PredefinedQuery.class.getResource(commonQueryFile), dtdFile);
+      commonDom = XmlUtil2.getValidatedXml(PredefinedQuery.class.getResource(commonQueryFile), dtdFile);
       log.info("Loaded predefined queries from file: " + commonQueryFile);
       if (dialectQueryFile != null)
       {
-        dialectDom = XMLUtil.getValidatedXml(PredefinedQuery.class.getResource(dialectQueryFile), dtdFile);
+        dialectDom = XmlUtil2.getValidatedXml(PredefinedQuery.class.getResource(dialectQueryFile), dtdFile);
         log.info("Loaded predefined queries from file: " + dialectQueryFile);
       }
@@ -142 +142 @@
     throws BaseException
   {
+    XPathExpression findQuery = XPathFactory.instance().compile("//query[@id='"+name+"']");
+  
     Element query = null;
-    try
-    {
-      XPath findQuery = XPath.newInstance("//query[@id='"+name+"']");
-  
-      if (dialectDom != null) query = (Element)findQuery.selectSingleNode(dialectDom);
-      if (query == null) query = (Element)findQuery.selectSingleNode(commonDom);
-    }
-    catch (JDOMException ex)
-    {
-      throw new BaseException(ex);
-    }
+    if (dialectDom != null) query = (Element)findQuery.evaluateFirst(dialectDom);
+    if (query == null) query = (Element)findQuery.evaluateFirst(commonDom);
+    
     if (query == null)
     {

trunk/src/core/net/sf/basedb/core/Presets.java

@@ -22 +22 @@
 package net.sf.basedb.core;
 
-import net.sf.basedb.util.XMLUtil;
+import net.sf.basedb.util.XmlUtil2;
 
 import java.util.ArrayList;
@@ -34 +34 @@
 import java.net.URL;
 
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.output.Format;
-import org.jdom.output.XMLOutputter;
+import org.jdom2.Document;
+import org.jdom2.Element;
+import org.jdom2.output.Format;
+import org.jdom2.output.XMLOutputter;
 
 /**
@@ -95 +95 @@
     try
     {
-      Document dom = XMLUtil.getValidatedXml(xml, dtdFile);
+      Document dom = XmlUtil2.getValidatedXml(xml, dtdFile);
       loadPresets(dom);
     }
@@ -115 +115 @@
     try
     {
-      Document dom = XMLUtil.getValidatedXML(in, dtdFile, filename);
+      Document dom = XmlUtil2.getValidatedXML(in, dtdFile, filename);
       loadPresets(dom);
     }
@@ -156 +156 @@
   private Document buildDocument()
   {
-    Document dom = XMLUtil.createDom("presets", "presets.dtd");
+    Document dom = XmlUtil2.createDom("presets", "presets.dtd");
     Element root = dom.getRootElement();
     if (defaultPreset != null)
@@ -212 +212 @@
     Parse an XML Document and load all presets.
   */
-  @SuppressWarnings("unchecked")
   private void loadPresets(Document dom)
   {
@@ -263 +262 @@
       @param preset
     */
-    @SuppressWarnings("unchecked")
     private Preset(Element preset)
     {

trunk/src/core/net/sf/basedb/core/RawDataTypes.java

@@ -28 +28 @@
 import net.sf.basedb.core.dbengine.DbEngine;
 import net.sf.basedb.util.Values;
-import net.sf.basedb.util.XMLUtil;
+import net.sf.basedb.util.XmlUtil2;
 
 import java.util.Comparator;
@@ -43 +43 @@
 import java.util.Collection;
 
-import org.jdom.Document;
-import org.jdom.Element;
+import org.jdom2.Document;
+import org.jdom2.Element;
 
 /**
@@ -165 +165 @@
       for (String xmlFile : files)
       {
-        Document dom = XMLUtil.getValidatedXml(RawDataTypes.class.getResource(xmlFile), dtdFile);
+        Document dom = XmlUtil2.getValidatedXml(RawDataTypes.class.getResource(xmlFile), dtdFile);
         loadRawDataTypes(dom, xmlFile);
         log.info("Loaded raw data types from file: " + xmlFile);
@@ -334 +334 @@
     {@link #rawDataTypes} map.
   */
-  @SuppressWarnings({"unchecked"})
   private static void loadRawDataTypes(Document dom, String xmlFile)
   {
@@ -346 +345 @@
       String description = Values.getStringOrNull(el.getAttributeValue("description"));
       String table = Values.getStringOrNull(el.getAttributeValue("table"));
-      int channels = XMLUtil.getIntAttribute(el, "channels", 2);
+      int channels = XmlUtil2.getIntAttribute(el, "channels", 2);
       
       if (!ExtendedProperty.isValidName(id))
@@ -396 +395 @@
     return a list of {@link RawDataProperty} objects.
   */
-  @SuppressWarnings({"unchecked"})
   private static List<RawDataProperty> loadProperties(Element rawDataTypeElement, int channels, String xmlFile)
   {
@@ -434 +432 @@
       String description = Values.getStringOrNull(property.getAttributeValue("description"));
       Type type = Type.fromValue(property.getAttributeValue("type"));
-      int length = XMLUtil.getIntAttribute(property, "length", 255);
+      int length = XmlUtil2.getIntAttribute(property, "length", 255);
       if (type == Type.STRING && length > 255) type = Type.TEXT;
-      boolean nullable = XMLUtil.getBooleanAttribute(property, "null", true);
+      boolean nullable = XmlUtil2.getBooleanAttribute(property, "null", true);
       String avgMethod = property.getAttributeValue("averagemethod");
       Formula.AverageMethod averageMethod = null;
@@ -451 +449 @@
         averageMethod = Formula.AverageMethod.NONE;       
       }
-      int channel = XMLUtil.getIntAttribute(property, "channel", 0);
+      int channel = XmlUtil2.getIntAttribute(property, "channel", 0);
       if (channel < 0 || channel > channels)
       {
@@ -467 +465 @@
     return a list of {@link IntensityFormula} objects.
   */
-  @SuppressWarnings({"unchecked"})
   private static List<IntensityFormula> loadIntensityFormulas(Element rawDataTypeElement, int channels, String xmlFile)
   {
@@ -494 +491 @@
       for (Element expression :  (List<Element>)formula.getChildren("formula"))
       {
-        int channel = XMLUtil.getIntAttribute(expression, "channel", 0);
+        int channel = XmlUtil2.getIntAttribute(expression, "channel", 0);
         String exp = Values.getStringOrNull(expression.getAttributeValue("expression"));
         if (channel <= 0 || channel > channels)

trunk/src/core/net/sf/basedb/util/XMLUtil.java

@@ -53 +53 @@
   @version 2.0
   @base.modified $Date$
+  @deprecated In 3.4, use {@link XmlUtil2} instead
 */
+@Deprecated
 public class XMLUtil
 {

trunk/src/core/net/sf/basedb/util/extensions/manager/processor/PluginInstallationProcessor.java

@@ -27 +27 @@
 import java.util.Map;
 
-import org.jdom.Element;
+import org.jdom2.Element;
 
 import net.sf.basedb.core.DbControl;
@@ -100 +100 @@
   }
 
-  @SuppressWarnings("unchecked")
   @Override
   public void processFile(ExtensionsManager manager, WriteableExtensionsFile wFile) 
@@ -166 +165 @@
         if (in != null)
         {
-          List<Element> configurations = PluginConfiguration.loadXmlFile(in, "META-INF/plugin-configurations.xml");
+          List<Element> configurations = PluginConfiguration.loadXmlFile2(in, "META-INF/plugin-configurations.xml");
           FileUtil.close(in);
           for (Element configuration : configurations)
@@ -199 +198 @@
                 config.setName(name);
                 config.setDescription(description);
-                config.setParameterValues((List<Element>)configuration.getChildren("parameter"));
+                config.setParameterValues2((List<Element>)configuration.getChildren("parameter"));
                 numConfigurations++;
               }

trunk/src/core/net/sf/basedb/util/extensions/xml/ExtensionPointFilter.java

@@ -24 +24 @@
 import java.util.regex.Pattern;
 
-import org.jdom.Element;
+import org.jdom2.Element;
 
 import net.sf.basedb.util.Values;

trunk/src/core/net/sf/basedb/util/extensions/xml/PluginDefinitionFilter.java

@@ -22 +22 @@
 package net.sf.basedb.util.extensions.xml;
 
-import org.jdom.Element;
+import org.jdom2.Element;
 
 import net.sf.basedb.util.filter.Filter;

trunk/src/core/net/sf/basedb/util/extensions/xml/XmlLoader.java

@@ -34 +34 @@
 import java.util.Set;
 
-import org.jdom.Attribute;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.Namespace;
-import org.jdom.output.Format;
-import org.jdom.output.XMLOutputter;
+import org.jdom2.Attribute;
+import org.jdom2.Document;
+import org.jdom2.Element;
+import org.jdom2.JDOMException;
+//import org.jdom2.JDOMException;
+import org.jdom2.Namespace;
+import org.jdom2.output.Format;
+import org.jdom2.output.XMLOutputter;
 
 import net.sf.basedb.core.BaseException;
@@ -49 +50 @@
 import net.sf.basedb.util.ClassUtil;
 import net.sf.basedb.util.Values;
-import net.sf.basedb.util.XMLUtil;
+import net.sf.basedb.util.XmlUtil2;
 import net.sf.basedb.util.extensions.AboutBean;
 import net.sf.basedb.util.extensions.Action;
@@ -258 +259 @@
   public About loadXmlFile(InputStream xmlFile, String filename,
       ClassLoader classLoader, boolean clear)
-    throws JDOMException, IOException, ClassNotFoundException, NoSuchMethodException,
+    throws IOException, ClassNotFoundException, NoSuchMethodException,
       IllegalAccessException, InstantiationException
   {
@@ -279 +280 @@
   */
   public About validateXmlFile(InputStream xmlFile, String filename)
-    throws IOException, JDOMException
+    throws IOException
   {
     validatedDom = null;
@@ -465 +466 @@
   */
   protected Document loadDocument(InputStream xmlFile, String filename)
-    throws IOException, JDOMException
+    throws IOException
   {
     log.debug("Validating file: " + filename);
-    Document dom = XMLUtil.getSchemaValidatedXML(xmlFile, filename, NAMESPACE, SCHEMA_FILE_URL);
-    return dom;
+    return XmlUtil2.getSchemaValidatedXML(xmlFile, filename, NAMESPACE, SCHEMA_FILE_URL);
   }
   
@@ -511 +511 @@
     @param aboutTag The about tag
   */
-  @SuppressWarnings("unchecked")
   protected AboutBean loadAbout(Element aboutTag)
   {
@@ -529 +528 @@
       about.setUrl(Values.getStringOrNull(aboutTag.getChildText("url", ns)));
       
-      List<Attribute> attributes = (List<Attribute>)aboutTag.getAttributes();
+      List<Attribute> attributes = aboutTag.getAttributes();
       for (Attribute a : attributes)
       {
@@ -800 +799 @@
     @since 3.0
   */
-  @SuppressWarnings("unchecked")
   protected int loadPluginDefinitions(Document dom, ClassLoader classLoader, About globalAbout)
     throws ClassNotFoundException, NoSuchMethodException,
@@ -873 +871 @@
           if (settingsTag != null)
           {
-            for (Element propertyTag : (List<Element>)settingsTag.getChildren("property", ns))
+            for (Element propertyTag : settingsTag.getChildren("property", ns))
             {
               String name = propertyTag.getAttributeValue("name");
@@ -929 +927 @@
     @param root The root element, if null nothing is done
   */
-  @SuppressWarnings("unchecked")
   protected void initBeanWithReflection(Object bean, Element root)
   {
@@ -935 +932 @@
     Class<?> beanClass = bean.getClass();
     
-    List<Element> parameters = (List<Element>)root.getChildren();
+    List<Element> parameters = root.getChildren();
     factoryParameters.put(bean, xmlOut.outputString(root));
     

trunk/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

@@ -73 +73 @@
 import net.sf.basedb.util.FileUtil;
 import net.sf.basedb.util.Values;
-import net.sf.basedb.util.XMLUtil;
+import net.sf.basedb.util.XmlUtil2;
 import net.sf.basedb.util.basefile.BaseFileWriter;
 import net.sf.basedb.util.export.spotdata.Base1FieldConverter;
@@ -87 +87 @@
 import net.sf.basedb.util.parser.FlatFileParser;
 
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.filter.ElementFilter;
-import org.jdom.output.Format;
-import org.jdom.output.XMLOutputter;
+import org.jdom2.Document;
+import org.jdom2.Element;
+//import org.jdom2.JDOMException;
+import org.jdom2.filter.ElementFilter;
+import org.jdom2.output.Format;
+import org.jdom2.output.XMLOutputter;
 
 import java.io.ByteArrayOutputStream;
@@ -1018 +1018 @@
   }
 
-
-  @SuppressWarnings({ "unchecked" })
   private Map<String, JobParameter> getJobParameterObjectsFromXML(String xml, boolean hideRemoved)
   {
@@ -1025 +1023 @@
     {
       String doctype = "<!DOCTYPE jobparameters SYSTEM \"base1-plugin-configuration-file.dtd\">";
-      Document doc = XMLUtil.getValidatedXml(doctype+xml, dtdFile);
+      Document doc = XmlUtil2.getValidatedXml(doctype+xml, dtdFile);
       Iterator<Element> it = doc.getDescendants(new ElementFilter("parameter"));
       Map<String, JobParameter> pars = new TreeMap<String, JobParameter>();
@@ -1044 +1042 @@
       return pars;
     }
-    catch (JDOMException e1)
-    {
-      throw new BaseException(e1.getCause());
-    }
     catch (IOException e1)
     {
@@ -1054 +1048 @@
   }
 
-
-  @SuppressWarnings({ "unchecked" })
   private List<PluginParameter<?>> getJobParametersFromXML(String xml, boolean hideRemoved)
   {
@@ -1061 +1053 @@
     {
       String doctype = "<!DOCTYPE jobparameters SYSTEM \"base1-plugin-configuration-file.dtd\">";
-      Document doc = XMLUtil.getValidatedXml(doctype+xml, dtdFile);
+      Document doc = XmlUtil2.getValidatedXml(doctype+xml, dtdFile);
       Iterator<Element> it = doc.getDescendants(new ElementFilter("parameter"));
       Map<Integer, PluginParameter<?>> positionParameter = 
@@ -1080 +1072 @@
       }
       return new ArrayList<PluginParameter<?>>(positionParameter.values());
-    }
-    catch (JDOMException e1)
-    {
-      throw new BaseException(e1.getCause());
     }
     catch (IOException e1)
@@ -1577 +1565 @@
     }
 
-    @SuppressWarnings({ "unchecked" })
     JobParameter(Element e)
     {
-      try
-      {
-        position = e.getAttribute("position").getIntValue();
+        position = XmlUtil2.getIntAttribute(e, "position", 1);
         type = Base1JobParameterType.get(e.getAttribute("type").getValue().charAt(0));
         Iterator<Element> it = e.getDescendants(new ElementFilter());
@@ -1624 +1609 @@
           }
         }
-      }
-      catch (JDOMException ex)
-      {
-        throw new BaseException(ex);
-      }
     }
 

trunk/src/plugins/core/net/sf/basedb/plugins/HelpExporter.java

@@ -61 +61 @@
 import java.util.Set;
 
-import org.jdom.DocType;
-import org.jdom.Element;
-import org.jdom.output.Format;
-import org.jdom.output.XMLOutputter;
+import org.jdom2.DocType;
+import org.jdom2.Element;
+import org.jdom2.output.Format;
+import org.jdom2.output.XMLOutputter;
 
 /**

trunk/src/plugins/core/net/sf/basedb/plugins/HelpImporter.java

@@ -66 +66 @@
 import net.sf.basedb.core.signal.SignalTarget;
 import net.sf.basedb.core.signal.ThreadSignalHandler;
-import net.sf.basedb.util.XMLUtil;
-
-import org.jdom.Document;
-import org.jdom.Element;
+import net.sf.basedb.util.XmlUtil2;
+
+import org.jdom2.Document;
+import org.jdom2.Element;
 
 /**
@@ -325 +325 @@
 
   @Override
-  @SuppressWarnings("unchecked")
   public void doImport(InputStream in, ProgressReporter progress)
     throws BaseException
@@ -343 +342 @@
         filename = f.getPath().toString();
       }
-      Document doc = XMLUtil.getValidatedXML(in, dtdURL, filename);     
+      Document doc = XmlUtil2.getValidatedXML(in, dtdURL, filename);      
       Element rootElement = doc.getRootElement();
       String clientExternalID = rootElement.getAttributeValue("clientExternalID");
@@ -349 +348 @@
       if(client.getExternalId().equals(clientExternalID))
       {
-        List<Element> helpElements = (List<Element>)rootElement.getChildren();  
+        List<Element> helpElements = rootElement.getChildren(); 
         float percentPerItem = 100.0f / helpElements.size();
         

trunk/src/plugins/core/net/sf/basedb/plugins/PluginConfigurationExporter.java

@@ -66 +66 @@
 import java.util.Set;
 
-import org.jdom.DocType;
-import org.jdom.Element;
-import org.jdom.output.Format;
-import org.jdom.output.XMLOutputter;
+import org.jdom2.DocType;
+import org.jdom2.Element;
+import org.jdom2.output.Format;
+import org.jdom2.output.XMLOutputter;
 
 /**

trunk/src/plugins/core/net/sf/basedb/plugins/PluginConfigurationImporter.java

@@ -65 +65 @@
 import java.util.jar.JarFile;
 
-import org.jdom.Element;
-import org.jdom.JDOMException;
+import org.jdom2.Element;
 
 /**
@@ -339 +338 @@
 
   @Override
-  @SuppressWarnings("unchecked")
   public void doImport(InputStream in, ProgressReporter progress) 
     throws BaseException
@@ -354 +352 @@
       }
       
-      List<Element> configurations = PluginConfiguration.loadXmlFile(in, filePath);
+      List<Element> configurations = PluginConfiguration.loadXmlFile2(in, filePath);
       int parameternumber = 0;
       for (Element configuration : configurations)
@@ -378 +376 @@
             config.setName(name);
             config.setDescription(description);
-            config.setParameterValues((List<Element>)configuration.getChildren("parameter"));
+            config.setParameterValues2((List<Element>)configuration.getChildren("parameter"));
             dc.saveItem(config);
           }
@@ -434 +432 @@
   public void importPluginConfigurationsFromJar(String jarPath, String xmlPath, 
         HashMap<Integer, Boolean> configurations,  boolean importAll, boolean setPermissions) 
-    throws IOException, JDOMException, BaseException
+    throws IOException, BaseException
   {
     this.importAll = importAll;
@@ -490 +488 @@
         
         in = file.getDownloadStream(0);
-        List<Element> configurations = PluginConfiguration.loadXmlFile(in, filePath);
+        List<Element> configurations = PluginConfiguration.loadXmlFile2(in, filePath);
         FileUtil.close(in);
         

trunk/src/plugins/core/net/sf/basedb/plugins/executor/ParameterDefinition.java

@@ -34 +34 @@
 import java.util.Set;
 
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.filter.ElementFilter;
-import org.jdom.output.Format;
-import org.jdom.output.XMLOutputter;
+import org.jdom2.Document;
+import org.jdom2.Element;
+import org.jdom2.filter.ElementFilter;
+import org.jdom2.output.Format;
+import org.jdom2.output.XMLOutputter;
 
 import net.sf.basedb.core.AnnotationType;
@@ -59 +58 @@
 import net.sf.basedb.core.query.Orders;
 import net.sf.basedb.util.Values;
-import net.sf.basedb.util.XMLUtil;
+import net.sf.basedb.util.XmlUtil2;
 
 /**
@@ -102 +101 @@
     @return A list with parameter definition
   */
-  @SuppressWarnings("unchecked")
   public static List<ParameterDefinition> parseXml(String xml, boolean validate)
   {
@@ -114 +112 @@
     try
     {
-      Document doc = XMLUtil.getXml(xml, dtdFile, validate);
+      Document doc = XmlUtil2.getXml(xml, dtdFile, validate);
       parameters = new ArrayList<ParameterDefinition>(doc.getContentSize());
       Iterator<Element> it = doc.getDescendants(new ElementFilter("parameter"));
@@ -124 +122 @@
         pd.setType(e.getAttributeValue("type"));
         pd.setName(e.getAttributeValue("name"));
-        pd.setRequired(XMLUtil.getBooleanAttribute(e, "required", false));
-        pd.setMultiple(XMLUtil.getBooleanAttribute(e, "multiple", false));
+        pd.setRequired(XmlUtil2.getBooleanAttribute(e, "required", false));
+        pd.setMultiple(XmlUtil2.getBooleanAttribute(e, "multiple", false));
         pd.setDefaultValue(Values.getStringOrNull(e.getChildText("default")));
         pd.setDescription(Values.getStringOrNull(e.getChildText("description")));
@@ -144 +142 @@
         parameters.add(pd);
       }
-    }
-    catch (JDOMException e)
-    {
-      throw new BaseException(e);
     }
     catch (IOException e)

trunk/src/test/TestXMLUtil.java

@@ -21 +21 @@
   along with BASE. If not, see <http://www.gnu.org/licenses/>.
 */
-import net.sf.basedb.util.XMLUtil;
+import net.sf.basedb.util.XmlUtil2;
 
 public class TestXMLUtil
@@ -53 +53 @@
     try
     {
-      org.jdom.Document dom = XMLUtil.getValidatedXml(xmlFile, dtdFile);
+      org.jdom2.Document dom = XmlUtil2.getValidatedXml(xmlFile, dtdFile);
       if (!TestUtil.getSilent()) write(dom.toString());
       write("--Create DOM OK");
@@ -69 +69 @@
     try
     {
-      org.jdom.Document dom = XMLUtil.getSchemaValidatedXML(xmlFile, schemaFiles);
+      org.jdom2.Document dom = XmlUtil2.getSchemaValidatedXML(xmlFile, schemaFiles);
       if (!TestUtil.getSilent()) write(dom.toString());
       write("--Create schema validated DOM OK");

trunk/src/test/data/JarPluginManifest.txt

@@ -1 +1 @@
 Class-Path: ../../lib/dist/AffxFusion.jar 
- ../../lib/dist/hibernate3.jar
+ ../../lib/dist/hibernate-core-4.3.5.Final.jar