
               +----------------------------------------+
               |     Cocoon Purity Problems List        |
               +----------------------------------------+
               

Cut&Paste
---------

The following is the run of the PMC cut & paste analysis tool set at default 75
tile size ran.

Run: 20030227


=============================================================
A 9 line (76 tokens) duplication:
Starting at line 142 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\acting\FormValidatorAction.java
Starting at line 126 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\acting\SessionValidatorAction.java
        boolean reloadable = Constants.DESCRIPTOR_RELOADABLE_DEFAULT;
        if (this.settings.containsKey("reloadable")) {
            reloadable = Boolean.valueOf((String) this.settings.get("reloadable")).booleanValue();
        }

        // read local settings
        try {
            Configuration conf = this.getConfiguration (
                    parameters.getParameter ("descriptor", (String) this.settings.get("descriptor")), resolver,
            parameters.getParameterAsBoolean("reloadable", reloadable));
=============================================================
A 7 line (78 tokens) duplication:
Starting at line 127 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\output\SessionAttributeOutputModule.java
Starting at line 126 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\output\RequestAttributeOutputModule.java
    public void rollback( Configuration modeConf, Map objectModel, Exception e ) {
        if (this.settings.get("isolation-level","0").equals("1")) {
            if (getLogger().isDebugEnabled())
                getLogger().debug("rolling back");
            this.rollback(objectModel, TRANS_PREFIX);
        } else {

            if (getLogger().isDebugEnabled())
=============================================================
A 34 line (79 tokens) duplication:
Starting at line 381 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\flow\javascript\JavaScriptInterpreter.java
Starting at line 531 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\flow\javascript\JavaScriptInterpreter.java
      while (value instanceof Wrapper) {
	  value = ((Wrapper)value).unwrap();
      }
      if (value instanceof Exception) {
	  Exception e = (Exception)value;
	  e.printStackTrace();
	  throw e;
      } else if (value instanceof Error) {
	  throw (Error)value;
      }
      throw ex;
    } catch (Exception ex) {
      ex.printStackTrace();
      throw ex;
    }
    finally {
      exitContext(thrScope);
    }
  }

  /**
   * Reloads any modified script files.
   *
   * <p>It checks to see if any of the files already read in (those
   * present in the <code>scripts</code> hash map) have been
   * modified.
   *
   * <p>It also checks to see if any script files have been registered
   * with the interpreter since the last call to
   * <code>checkForModifiedScripts</code>. These files are stored in
   * the temporary array <code>needResolve</code>. If any such files
   * are found, they are read in.
   *
   * @param environment an <code>Environment</code> value
   */
=============================================================
A 8 line (79 tokens) duplication:
Starting at line 155 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\DigestMetaModule.java
Starting at line 252 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\DigestMetaModule.java
        int encode = ((Integer) encodingNames.get(this.defaultEncode)).intValue();
        if (modeConf!=null) {
            inputName   = modeConf.getChild("input-module").getAttribute("name",null);
            if (inputName != null) {
                inputConfig = modeConf.getChild("input-module");
            }
            // read necessary parameters
            algorithm = modeConf.getAttribute("algorithm", algorithm);
            provider  = modeConf.getAttribute("provider", provider);
=============================================================
A 21 line (82 tokens) duplication:
Starting at line 176 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\JXPathMetaModule.java
Starting at line 153 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\AbstractJXPathModule.java
                        getLogger().debug("adding Class "+clazzName+" to functions");
                    lib.addFunctions(new ClassFunctions(clazz, prefix));
                } catch (ClassNotFoundException cnf) {
                    if (getLogger().isWarnEnabled())
                        getLogger().warn("Class not found: "+clazzName);
                }
            } else {
                if (getLogger().isWarnEnabled())
                    getLogger().warn("Class name or prefix null: "+clazzName+" / "+prefix);
            }
        }
    }


    /**
     * Register all extension packages listed in the configuration
     * through <code>&lt;package name="fully.qualified.package"
     * prefix="prefix"/&gt;</code> in the given FunctionLibrary.
     *
     * @param lib a <code>FunctionLibrary</code> value
     * @param conf a <code>Configuration</code> value
     */
=============================================================
A 15 line (86 tokens) duplication:
Starting at line 78 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\selection\RequestAttributeSelector.java
Starting at line 77 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\selection\SessionAttributeSelector.java
  implements Configurable, ThreadSafe, Selector {

    protected String defaultName;

    public void configure(Configuration config) throws ConfigurationException {
        this.defaultName = config.getChild("attribute-name").getValue(null);
    }

    public boolean select(String expression, Map objectModel, Parameters parameters) {
        String name = parameters.getParameter("attribute-name", this.defaultName);

        if (name == null) {
            getLogger().warn("No attribute name given -- failing.");
            return false;
        }

=============================================================
A 16 line (86 tokens) duplication:
Starting at line 100 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\treeprocessor\sitemap\TransformNode.java
Starting at line 106 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\treeprocessor\sitemap\GenerateNode.java
                : VariableResolver.buildParameters(this.pipelineHints, context, objectModel)
        );

        // Check view
        if (this.views != null) {
	   
            //inform the pipeline that we have a branch point
            context.getProcessingPipeline().informBranchPoint();
	    
            String cocoonView = env.getView();
            if (cocoonView != null) {

                // Get view node
                ProcessingNode viewNode = (ProcessingNode)this.views.get(cocoonView);

                if (viewNode != null) {
                    if (getLogger().isInfoEnabled()) {
=============================================================
A 6 line (89 tokens) duplication:
Starting at line 456 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\transformation\SourceWritingTransformer.java
Starting at line 495 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\transformation\SourceWritingTransformer.java
                tag = (String)this.stack.pop();
                if (tag.equals("PATH") == true) {
                    path = (String)this.stack.pop();
                } else if (tag.equals("FILE") == true) {
                    fileName = (String)this.stack.pop();
                } else if (tag.equals("FRAGMENT") == true) {
                    fragment = (DocumentFragment)this.stack.pop();
=============================================================
A 95 line (96 tokens) duplication:
Starting at line 117 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\generation\LinkStatusGenerator.java
Starting at line 92 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\crawler\SimpleCocoonCrawlerImpl.java
    public final static String LINK_CONTENT_TYPE_CONFIG = "link-content-type";

    /**
     * Default value of <code>link-content-type</code> configuration value.
     * <p>
     *   Its value is <code>application/x-cocoon-links</code>.
     * </p>
     *
     * @since
     */
    public final String LINK_CONTENT_TYPE_DEFAULT = "application/x-cocoon-links";

    /**
     * Config element name specifying query-string appendend for requesting links
     * of an URL.
     * <p>
     *  Its value is <code>link-view-query</code>.
     * </p>
     *
     * @since
     */
    public final static String LINK_VIEW_QUERY_CONFIG = "link-view-query";
    /**
     * Default value of <code>link-view-query</code> configuration value.
     * <p>
     *   Its value is <code>?cocoon-view=links</code>.
     * </p>
     *
     * @since
     */
    public final static String LINK_VIEW_QUERY_DEFAULT = "cocoon-view=links";

    /**
     * Config element name specifying excluding regular expression pattern.
     * <p>
     *  Its value is <code>exclude</code>.
     * </p>
     *
     * @since
     */
    public final static String EXCLUDE_CONFIG = "exclude";

    /**
     * Config element name specifying including regular expression pattern.
     * <p>
     *  Its value is <code>include</code>.
     * </p>
     *
     * @since
     */
    public final static String INCLUDE_CONFIG = "include";

    /**
     * Config element name specifying http header value for user-Agent.
     * <p>
     *  Its value is <code>user-agent</code>.
     * </p>
     *
     * @since
     */
    public final static String USER_AGENT_CONFIG = "user-agent";
    /**
     * Default value of <code>user-agent</code> configuration value.
     *
     * @see org.apache.cocoon.Constants#COMPLETE_NAME
     * @since
     */
    public final static String USER_AGENT_DEFAULT = Constants.COMPLETE_NAME;

    /**
     * Config element name specifying http header value for accept.
     * <p>
     *  Its value is <code>accept</code>.
     * </p>
     *
     * @since
     */
    public final static String ACCEPT_CONFIG = "accept";
    /**
     * Default value of <code>accept</code> configuration value.
     * <p>
     *   Its value is <code>* / *</code>
     * </p>
     *
     * @since
     */
    public final static String ACCEPT_DEFAULT = "*/*";

    private String linkViewQuery = LINK_VIEW_QUERY_DEFAULT;
    private String linkContentType = LINK_CONTENT_TYPE_DEFAULT;
    private HashSet excludeCrawlingURL;
    private HashSet includeCrawlingURL;
    private String userAgent = USER_AGENT_DEFAULT;
    private String accept = ACCEPT_DEFAULT;

    private HashSet crawled;
=============================================================
A 19 line (100 tokens) duplication:
Starting at line 81 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\matching\RegexpSessionAttributeMatcher.java
Starting at line 82 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\matching\WildcardSessionAttributeMatcher.java
            getLogger().debug("Default attribute-name is = '" + this.defaultParam + "'");
        }
    }

    protected String getMatchString(Map objectModel, Parameters parameters) {

        String paramName = parameters.getParameter("attribute-name", this.defaultParam);
        if (paramName == null) {
            getLogger().warn("No attribute name given. FAILING");
            return null;
        }

        Object result = ObjectModelHelper.getRequest(objectModel).getSession().getAttribute(paramName);
        if (result == null) {
            getLogger().debug("Session attribute '" + paramName + "' not set.");
            return null;
        }

        return result.toString();
    }
=============================================================
A 10 line (100 tokens) duplication:
Starting at line 164 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\DigestMetaModule.java
Starting at line 261 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\DigestMetaModule.java
            salt  = modeConf.getAttribute("salt", salt);
            encode = ((Integer) encodingNames.get(modeConf.getAttribute("encode", this.defaultEncode))).intValue();

            // preferred
            algorithm = modeConf.getChild("algorithm").getValue(algorithm);
            provider  = modeConf.getChild("provider").getValue(provider);
            salt  = modeConf.getChild("salt").getValue(salt);
            encode = ((Integer) encodingNames.get(modeConf.getChild("encode").getValue(this.defaultEncode))).intValue();
        }


=============================================================
A 12 line (101 tokens) duplication:
Starting at line 353 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\transformation\SourceWritingTransformer.java
Starting at line 373 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\transformation\SourceWritingTransformer.java
            if (attr.getValue(CREATE_ATTRIBUTE) != null
                && attr.getValue(CREATE_ATTRIBUTE).equals("false")) {
                this.stack.push("false");
            } else {
                this.stack.push("true");
            }
            if (attr.getValue(OVERWRITE_ATTRIBUTE) != null
                && attr.getValue(OVERWRITE_ATTRIBUTE).equals("false")) {
                this.stack.push("false");
            } else {
                this.stack.push("true");
            }
            this.stack.push(attr.getValue(SERIALIZER_ATTRIBUTE));
=============================================================
A 21 line (113 tokens) duplication:
Starting at line 231 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\JXPathMetaModule.java
Starting at line 208 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\AbstractJXPathModule.java
                getLogger().debug("adding local Classes and Packages to functions");
            localLib = new FunctionLibrary();
            localLib.addFunctions(this.library);
            getPackages(localLib, conf);
            getFunctions(localLib, conf);
        } else {
            if (getLogger().isDebugEnabled())
                getLogger().debug("no local Classes or Packages");
            localLib = this.library;
        }
        
        context.setFunctions(localLib);
    }


    public Object getAttribute(String name, Configuration modeConf,
                               Map objectModel)
        throws ConfigurationException {

        Object contextObj = getContextObject(modeConf, objectModel);
        if (contextObj == null) return null;
        if (modeConf != null) {
=============================================================
A 23 line (115 tokens) duplication:
Starting at line 101 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\RequestParameterModule.java
Starting at line 101 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\RequestAttributeModule.java
Starting at line 101 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\SessionAttributeModule.java
Starting at line 100 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\HeaderAttributeModule.java
        Request request = ObjectModelHelper.getRequest(objectModel);
        String wildcard = name;
        if ( modeConf != null ) {
            wildcard = modeConf.getAttribute( "parameter", wildcard );
            // preferred
            wildcard = modeConf.getChild("parameter").getValue(wildcard);
        }
        int wildcardIndex = wildcard.indexOf( "*" );
        if ( wildcardIndex != -1 ) {
            // "*" contained in parameter name => combine all
            // parameters' values that match prefix, suffix

            // split the parameter's name so that the "*" could be
            // determined by looking at the parameters' names that
            // start with the prefix and end with the suffix
            //
            String prefix = wildcard.substring( 0, wildcardIndex );
            String suffix;
            if ( wildcard.length() >= wildcardIndex + 1 ) {
                suffix = wildcard.substring( wildcardIndex + 1 );
            } else {
                suffix = "";
            }
            List values = new LinkedList();
=============================================================
A 14 line (121 tokens) duplication:
Starting at line 255 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\generation\StatusGenerator.java
Starting at line 291 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\generation\StatusGenerator.java
                    ch.startElement(namespace, "line", "line", atts);
                    ch.characters(line.toCharArray(), 0, line.length());
                    ch.endElement(namespace, "line", "line");
                }
            }

            if (size == 0) {
                ch.startElement(namespace, "line", "line", atts);
                String value = "[empty]";
                ch.characters(value.toCharArray(), 0, value.length());
                ch.endElement(namespace, "line", "line");
            }
            ch.endElement(namespace, "value", "value");

            addValue(ch, "size", String.valueOf(size) + " items in cache (" + empty + " are empty)");
=============================================================
A 20 line (125 tokens) duplication:
Starting at line 131 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\ProcessingException.java
Starting at line 149 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\CascadingIOException.java
            TransformerException transformerException = (TransformerException) t;
            SourceLocator sourceLocator = transformerException.getLocator();
            
            if( null != sourceLocator ) {
                sb.append( String.valueOf(sourceLocator.getSystemId()));
                sb.append( ":" );
                sb.append( String.valueOf(sourceLocator.getLineNumber()));
                sb.append( ":" );
                sb.append( String.valueOf(sourceLocator.getColumnNumber()));
                sb.append( ":" );
            }
        }
        return sb.toString();
    }
    
    public void printStackTrace() {
        super.printStackTrace();
        if(getCause()!=null)
            getCause().printStackTrace();
    }
    
=============================================================
A 21 line (127 tokens) duplication:
Starting at line 174 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\output\SessionAttributeOutputModule.java
Starting at line 173 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\output\RequestAttributeOutputModule.java
    public void commit( Configuration modeConf, Map objectModel ) {
        if (this.settings.get("isolation-level","0").equals("1")) {

            Logger logger = getLogger();
            if (logger.isDebugEnabled())
                logger.debug("prepare commit");

            Map aMap = this.prepareCommit(objectModel, TRANS_PREFIX);
            if (aMap == null) {
                return;
            }
            
            Iterator iter = aMap.keySet().iterator();
            if (!iter.hasNext()){
                return;
            }
            
            String prefix = (String) this.settings.get("key-prefix", PREFIX );
            if (prefix != "") {
                prefix = prefix+":";
            } else {
                prefix = null;
=============================================================
A 21 line (133 tokens) duplication:
Starting at line 279 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\JXPathMetaModule.java
Starting at line 253 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\AbstractJXPathModule.java
            java.beans.PropertyDescriptor[] properties = info.getPropertyDescriptors();
            java.util.List names = new java.util.LinkedList();
            for (int i = 0; i < properties.length; i++) {
                names.add(properties[i].getName());
            }
            return names.listIterator();
        } catch (Exception e) {
            throw new ConfigurationException(
                "Error retrieving attribute names for class: "
                + contextObj.getClass(),
                e
            );
        }

    }

    public Object[] getAttributeValues(String name, Configuration modeConf, Map objectModel)
        throws ConfigurationException {

        Object contextObj = getContextObject(modeConf, objectModel);
        if (contextObj == null) return null;
        if (modeConf != null) {
=============================================================
A 37 line (142 tokens) duplication:
Starting at line 280 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\xpath\XPathUtil.java
Starting at line 944 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\xml\dom\DOMUtil.java
                    while (i < l) {
                        if (xpath.charAt(i) == '/') {
                            result[components] = xpath.substring(start, i);
                            start = i+1;
                            components++;
                        }
                        i++;
                    }
                    result[components] = xpath.substring(start);
                }
            }
        }
        return result;
    }

    /**
     * Use a path to select the first occurence of a node. The namespace
     * of a node is ignored!
     * @param contextNode The node starting the search.
     * @param path        The path to search the node. The
     *                    contextNode is searched for a child named path[0],
     *                    this node is searched for a child named path[1]...
     * @param create      If a child with the corresponding name is not found
     *                    and create is set, this node will be created.
    */
    public static Node getFirstNodeFromPath(Node contextNode,
                                            final String[] path,
                                            final boolean  create) {
        if (contextNode == null || path == null || path.length == 0)
            return contextNode;
        // first test if the node exists
        Node item = getFirstNodeFromPath(contextNode, path, 0);
        if (item == null && create == true) {
            int i = 0;
            NodeList childs;
            boolean found;
            int m, l;
            while (contextNode != null && i < path.length) {
=============================================================
A 21 line (158 tokens) duplication:
Starting at line 156 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\xscript\XScriptManagerImpl.java
Starting at line 270 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\xscript\XScriptManagerImpl.java
                             int scope)
            throws IllegalArgumentException
    {
        XScriptObject o;
        XScriptVariableScope s = null;

        if (scope == XScriptManager.GLOBAL_SCOPE) {
            s = (XScriptVariableScope) ObjectModelHelper.getContext(objectModel).getAttribute(CONTEXT);
        } else if (scope == XScriptManager.SESSION_SCOPE) {
            Request request = ObjectModelHelper.getRequest(objectModel);
            s = (XScriptVariableScope) request.getSession().getAttribute(CONTEXT);
        } else if (scope == XScriptManager.REQUEST_SCOPE) {
            Request request = ObjectModelHelper.getRequest(objectModel);
            s = (XScriptVariableScope) request.getAttribute(CONTEXT);
        } else if (scope == XScriptManager.PAGE_SCOPE) {
            s = pageScope;
        } else if (scope == XScriptManager.ALL_SCOPES) {
            Request request = ObjectModelHelper.getRequest(objectModel);

            // Lookup in the request scope first.
            s = (XScriptVariableScope) request.getAttribute(CONTEXT);
            if (s != null) {
=============================================================
A 33 line (178 tokens) duplication:
Starting at line 200 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\JXPathMetaModule.java
Starting at line 177 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\AbstractJXPathModule.java
        Configuration[] children = conf.getChildren("package");
        int i = children.length;
        while (i-- >0) {
            String packageName = children[i].getAttribute("name",null);
            String prefix = children[i].getAttribute("prefix",null);
            if (packageName != null && prefix != null) {
                if (getLogger().isDebugEnabled())
                    getLogger().debug("adding Package "+packageName+" to functions");
                lib.addFunctions(new PackageFunctions(packageName, prefix));
            } else {
                if (getLogger().isWarnEnabled())
                    getLogger().warn("Package name or prefix null: "+packageName+" / "+prefix);
            }
        }
    }


    /**
     * Actually add global functions and packages as well as those
     * listed in the configuration object.
     *
     * @param context a <code>JXPathContext</code> value
     * @param conf a <code>Configuration</code> value holding local
     * packages and functions.
     */
    protected void setupExtensions(JXPathContext context, Configuration conf) {
        
        FunctionLibrary localLib = null;

        if (conf != null) {
            if (getLogger().isDebugEnabled())
                getLogger().debug("adding local Classes and Packages to functions");
            localLib = new FunctionLibrary();
            localLib.addFunctions(this.library);
=============================================================
A 21 line (180 tokens) duplication:
Starting at line 181 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\SimpleMappingMetaModule.java
Starting at line 242 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\SimpleMappingMetaModule.java
            mapping = new Mapping(modeConf);
            prefix = modeConf.getChild("prefix").getValue(null);
            suffix = modeConf.getChild("suffix").getValue(null);
            rmPrefix = modeConf.getChild("rm-prefix").getValue(null);
            rmSuffix = modeConf.getChild("rm-suffix").getValue(null);
        }
        
        // remove rm-prefix and rm-suffix
        if (rmPrefix != null && name.startsWith(rmPrefix)) {
            name = name.substring(rmPrefix.length());
        }
        if (rmSuffix != null && name.endsWith(rmSuffix)) {
            name = name.substring(0,name.length() - rmSuffix.length());
        }
        // map
        String param = mapping.mapTo(name);
        // add prefix and suffix
        if (prefix != null) param = prefix + param;
        if (suffix != null) param = param + suffix;
        if (getLogger().isDebugEnabled())
            getLogger().debug("mapping ['"+name+"'] to ['"+param+"']");

=============================================================
A 46 line (223 tokens) duplication:
Starting at line 318 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\xpath\XPathUtil.java
Starting at line 982 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\xml\dom\DOMUtil.java
                childs = contextNode.getChildNodes();
                found = false;
                if (childs != null) {
                    m = 0;
                    l = childs.getLength();
                    while (found == false && m < l) {
                        item = childs.item(m);
                        if (item.getNodeType() == Document.ELEMENT_NODE
                            && item.getLocalName().equals(path[i]) == true) {
                            found = true;
                            contextNode = item;
                        }
                        m++;
                    }
                }
                if (found == false) {
                    Element e = contextNode.getOwnerDocument().createElementNS(null, path[i]);
                    contextNode.appendChild(e);
                    contextNode = e;
                }
                i++;
            }
            item = contextNode;
        }
        return item;
    }

    /**
     * Private helper method for getFirstNodeFromPath()
     */
    private static Node getFirstNodeFromPath(final Node contextNode,
                                             final String[] path,
                                             final int      startIndex) {
        int i = 0;
        NodeList childs;
        boolean found;
        int l;
        Node item = null;

        childs = contextNode.getChildNodes();
        found = false;
        if (childs != null) {
            i = 0;
            l = childs.getLength();
            while (found == false && i < l) {
                item = childs.item(i);
                if (item.getNodeType() == Document.ELEMENT_NODE
=============================================================
A 28 line (250 tokens) duplication:
Starting at line 167 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\xpath\XPathUtil.java
Starting at line 741 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\xml\dom\DOMUtil.java
                        java.util.List attrValuePairs = new java.util.ArrayList(4);
                        boolean noError = true;

                        String attr;
                        String value;
                        // scan for attributes
                        java.util.StringTokenizer tokenizer = new java.util.StringTokenizer(XPathExp, "= ");
                        while (tokenizer.hasMoreTokens() == true) {
                            attr = tokenizer.nextToken();
                            if (attr.startsWith("@") == true) {
                                if (tokenizer.hasMoreTokens() == true) {
                                    value = tokenizer.nextToken();
                                    if (value.startsWith("'") && value.endsWith("'")) value = value.substring(1, value.length()-1);
                                    if (value.startsWith("\"") && value.endsWith("\"")) value = value.substring(1, value.length()-1);
                                    attrValuePairs.add(attr.substring(1));
                                    attrValuePairs.add(value);
                                } else {
                                    noError = false;
                                }
                            } else if (attr.trim().equals("and") == false) {
                                noError = false;
                            }
                        }
                        if (noError == true) {
                            for(int l=0;l<attrValuePairs.size();l=l+2) {
                                ((Element)newNode).setAttributeNS(null, (String)attrValuePairs.get(l),
                                                                (String)attrValuePairs.get(l+1));
                            }
                        }
=============================================================
A 53 line (291 tokens) duplication:
Starting at line 146 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\matching\modular\CachingRegexpMatcher.java
Starting at line 146 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\matching\modular\CachingWildcardMatcher.java
                                      +(this.inputSelector!=null&&this.inputSelector.hasComponent(this.defaultInput)?"known":"unknown"));
            }
        } catch (Exception e) {
            if (getLogger().isWarnEnabled()) 
                getLogger().warn("A problem occurred setting up '" + this.defaultInput + "': " + e.getMessage());
        }
    }


    public void dispose() {

        if (!this.initialized) 
            if (getLogger().isErrorEnabled()) 
                getLogger().error("Uninitialized Component! FAILING");
        else 
            if (this.inputSelector != null) {
                if (this.input != null)
                    this.inputSelector.release(this.input);
                this.manager.release(this.inputSelector);
            }
    }


    protected String getMatchString(Map objectModel, Parameters parameters) {

        String paramName = parameters.getParameter("parameter-name", this.defaultParam);
        String inputName = parameters.getParameter("input-module", this.defaultInput);

        if (!this.initialized) {
            if (getLogger().isErrorEnabled()) 
                getLogger().error("Uninitialized Component! FAILING");
            return null;
        }
        if (paramName == null) {
            if (getLogger().isWarnEnabled()) 
                getLogger().warn("No parameter name given. Trying to Continue");
        }
        if (inputName == null) {
            if (getLogger().isWarnEnabled()) 
                getLogger().warn("No input module given. FAILING");
            return null;
        }

        Object result = null;

        if (this.input != null && inputName.equals(this.defaultInput)) {
            // input module is thread safe
            // thus we still have a reference to it
            try {
                if (this.input != null) {
                    result = this.input.getAttribute(paramName, this.inputConf, objectModel);
                }
=============================================================
A 59 line (308 tokens) duplication:
Starting at line 103 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\ProcessingException.java
Starting at line 121 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\CascadingIOException.java
            s.append( extraInfo(t) );
            s.append(t.toString());
        }
        return s.toString();
    }
    
    /**
     * Examine Throwable and try to figure out location information.
     * <p>
     *   At the moment only SAXParseException, and TransformerException
     *   are considered.
     * </p>
     *
     * @return String containing location information of the format
     *  <code>{file-name}:{line}:{column}:</code>, if no location info is 
     *  available return empty string
     */
    private String extraInfo( Throwable t ) {
        StringBuffer sb = new StringBuffer();
        if (t instanceof SAXParseException) {
            SAXParseException spe = (SAXParseException)t;
            sb.append( String.valueOf(spe.getSystemId()));
            sb.append( ":" );
            sb.append( String.valueOf(spe.getLineNumber()));
            sb.append( ":" );
            sb.append( String.valueOf(spe.getColumnNumber()));
            sb.append( ":" );
        } else if (t instanceof TransformerException) {
            TransformerException transformerException = (TransformerException) t;
            SourceLocator sourceLocator = transformerException.getLocator();
            
            if( null != sourceLocator ) {
                sb.append( String.valueOf(sourceLocator.getSystemId()));
                sb.append( ":" );
                sb.append( String.valueOf(sourceLocator.getLineNumber()));
                sb.append( ":" );
                sb.append( String.valueOf(sourceLocator.getColumnNumber()));
                sb.append( ":" );
            }
        }
        return sb.toString();
    }
    
    public void printStackTrace() {
        super.printStackTrace();
        if(getCause()!=null)
            getCause().printStackTrace();
    }
    
    public void printStackTrace( PrintStream s ) {
        super.printStackTrace(s);
        if(getCause()!=null)
            getCause().printStackTrace(s);
    }
    
    public void printStackTrace( PrintWriter s ) {
        super.printStackTrace(s);
        if(getCause()!=null)
            getCause().printStackTrace(s);
    }
=============================================================
A 85 line (448 tokens) duplication:
Starting at line 167 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\JXPathMetaModule.java
Starting at line 144 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\components\modules\input\AbstractJXPathModule.java
        Configuration[] children = conf.getChildren("function");
        int i = children.length;
        while (i-- >0) {
            String clazzName = children[i].getAttribute("name",null);
            String prefix = children[i].getAttribute("prefix",null);
            if (clazzName != null && prefix != null) {
                try {
                    Class clazz = Class.forName(clazzName);
                    if (getLogger().isDebugEnabled())
                        getLogger().debug("adding Class "+clazzName+" to functions");
                    lib.addFunctions(new ClassFunctions(clazz, prefix));
                } catch (ClassNotFoundException cnf) {
                    if (getLogger().isWarnEnabled())
                        getLogger().warn("Class not found: "+clazzName);
                }
            } else {
                if (getLogger().isWarnEnabled())
                    getLogger().warn("Class name or prefix null: "+clazzName+" / "+prefix);
            }
        }
    }


    /**
     * Register all extension packages listed in the configuration
     * through <code>&lt;package name="fully.qualified.package"
     * prefix="prefix"/&gt;</code> in the given FunctionLibrary.
     *
     * @param lib a <code>FunctionLibrary</code> value
     * @param conf a <code>Configuration</code> value
     */
    protected void getPackages(FunctionLibrary lib, Configuration conf)  {

        Configuration[] children = conf.getChildren("package");
        int i = children.length;
        while (i-- >0) {
            String packageName = children[i].getAttribute("name",null);
            String prefix = children[i].getAttribute("prefix",null);
            if (packageName != null && prefix != null) {
                if (getLogger().isDebugEnabled())
                    getLogger().debug("adding Package "+packageName+" to functions");
                lib.addFunctions(new PackageFunctions(packageName, prefix));
            } else {
                if (getLogger().isWarnEnabled())
                    getLogger().warn("Package name or prefix null: "+packageName+" / "+prefix);
            }
        }
    }


    /**
     * Actually add global functions and packages as well as those
     * listed in the configuration object.
     *
     * @param context a <code>JXPathContext</code> value
     * @param conf a <code>Configuration</code> value holding local
     * packages and functions.
     */
    protected void setupExtensions(JXPathContext context, Configuration conf) {
        
        FunctionLibrary localLib = null;

        if (conf != null) {
            if (getLogger().isDebugEnabled())
                getLogger().debug("adding local Classes and Packages to functions");
            localLib = new FunctionLibrary();
            localLib.addFunctions(this.library);
            getPackages(localLib, conf);
            getFunctions(localLib, conf);
        } else {
            if (getLogger().isDebugEnabled())
                getLogger().debug("no local Classes or Packages");
            localLib = this.library;
        }
        
        context.setFunctions(localLib);
    }


    public Object getAttribute(String name, Configuration modeConf,
                               Map objectModel)
        throws ConfigurationException {

        Object contextObj = getContextObject(modeConf, objectModel);
        if (contextObj == null) return null;
        if (modeConf != null) {
=============================================================
A 138 line (758 tokens) duplication:
Starting at line 100 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\matching\modular\CachingRegexpMatcher.java
Starting at line 100 in C:\Code\cocoon-2.1.x\src\java\org\apache\cocoon\matching\modular\CachingWildcardMatcher.java
    private boolean initialized = false;
    private InputModule input = null;
    private ComponentSelector inputSelector = null;

    /**
     * Set the current <code>ComponentManager</code> instance used by this
     * <code>Composable</code>.
     */
    public void compose(ComponentManager manager) throws ComponentException {

        this.manager=manager;
    }


    public void configure(Configuration config) throws ConfigurationException {

        this.defaultParam = config.getChild("parameter-name").getValue(null);
        this.inputConf = config.getChild("input-module");
        this.defaultInput = this.inputConf.getAttribute("name",this.defaultInput);
    }


    public void initialize() {

        try {
            // obtain input module
            this.inputSelector=(ComponentSelector) this.manager.lookup(INPUT_MODULE_SELECTOR); 
            if (this.defaultInput != null && 
                this.inputSelector != null && 
                this.inputSelector.hasComponent(this.defaultInput)
                ){
                this.input = (InputModule) this.inputSelector.select(this.defaultInput);
                if (!(this.input instanceof ThreadSafe && this.inputSelector instanceof ThreadSafe) ) {
                    this.inputSelector.release(this.input);
                    this.manager.release(this.inputSelector);
                    this.input = null;
                    this.inputSelector = null;
                }
                this.initialized = true;
            } else {
                if (getLogger().isErrorEnabled())
                    getLogger().error("A problem occurred setting up '" + this.defaultInput 
                                      + "': Selector is "+(this.inputSelector!=null?"not ":"")
                                      +"null, Component is "
                                      +(this.inputSelector!=null&&this.inputSelector.hasComponent(this.defaultInput)?"known":"unknown"));
            }
        } catch (Exception e) {
            if (getLogger().isWarnEnabled()) 
                getLogger().warn("A problem occurred setting up '" + this.defaultInput + "': " + e.getMessage());
        }
    }


    public void dispose() {

        if (!this.initialized) 
            if (getLogger().isErrorEnabled()) 
                getLogger().error("Uninitialized Component! FAILING");
        else 
            if (this.inputSelector != null) {
                if (this.input != null)
                    this.inputSelector.release(this.input);
                this.manager.release(this.inputSelector);
            }
    }


    protected String getMatchString(Map objectModel, Parameters parameters) {

        String paramName = parameters.getParameter("parameter-name", this.defaultParam);
        String inputName = parameters.getParameter("input-module", this.defaultInput);

        if (!this.initialized) {
            if (getLogger().isErrorEnabled()) 
                getLogger().error("Uninitialized Component! FAILING");
            return null;
        }
        if (paramName == null) {
            if (getLogger().isWarnEnabled()) 
                getLogger().warn("No parameter name given. Trying to Continue");
        }
        if (inputName == null) {
            if (getLogger().isWarnEnabled()) 
                getLogger().warn("No input module given. FAILING");
            return null;
        }

        Object result = null;

        if (this.input != null && inputName.equals(this.defaultInput)) {
            // input module is thread safe
            // thus we still have a reference to it
            try {
                if (this.input != null) {
                    result = this.input.getAttribute(paramName, this.inputConf, objectModel);
                }
            } catch (Exception e) {
                if (getLogger().isWarnEnabled()) 
                    getLogger().warn("A problem occurred acquiring Parameter '" + paramName 
                                      + "' from '" + inputName + "': " + e.getMessage());
            }
        } else {
            // input was not thread safe
            // so acquire it again
            ComponentSelector iputSelector = null;
            InputModule iput = null;
            try {
                // obtain input module
                iputSelector=(ComponentSelector) this.manager.lookup(INPUT_MODULE_SELECTOR); 
                if (inputName != null && iputSelector != null && iputSelector.hasComponent(inputName)){
                    iput = (InputModule) iputSelector.select(inputName);
                }
                if (iput != null) {
                    result = iput.getAttribute(paramName, this.inputConf, objectModel);
                }
            } catch (Exception e) {
                if (getLogger().isWarnEnabled()) 
                    getLogger().warn("A problem occurred acquiring Parameter '" + paramName 
                                     + "' from '" + inputName + "': " + e.getMessage());
            } finally {
                // release components
                if (iputSelector != null) {
                    if (iput != null)
                        iputSelector.release(iput);
                    this.manager.release(iputSelector);
                }
            }
        }

        if (result instanceof String) {
            return (String) result;
        } else {
            return result.toString();
        }
    }