/src/edu/ucsb/nceas/metacat/MetaCatServlet.java - Annotate - Metacat - Ecoinformatics Redmine

metacat/src/edu/ucsb/nceas/metacat/MetaCatServlet.java @ 1299

-            jones
+/**
-            jones
+ *  '$RCSfile$'
  *    Purpose: A Class that implements a metadata catalog as a java Servlet
  *  Copyright: 2000 Regents of the University of California and the
  *             National Center for Ecological Analysis and Synthesis
-            berkley
+ *    Authors: Matt Jones, Dan Higgins, Jivka Bojilova, Chad Berkley
-            jones
+ *    Release: @release@
             jones
-            jones
+ *   '$Author$'
  *     '$Date$'
  * '$Revision$'
             jones
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
  * the Free Software Foundation; either version 2 of the License, or
  * (at your option) any later version.
+ *
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
+ *
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
-            jones
+ */
 package edu.ucsb.nceas.metacat;
-            jones
+import com.oreilly.servlet.multipart.FilePart;
 import com.oreilly.servlet.multipart.MultipartParser;
 import com.oreilly.servlet.multipart.ParamPart;
 import com.oreilly.servlet.multipart.Part;
-            bojilova
+import java.io.File;
-            jones
+import java.io.PrintWriter;
 import java.io.IOException;
-            jones
+import java.io.StringReader;
-            jones
+import java.io.FileInputStream;
-            bojilova
+import java.io.BufferedInputStream;
-            jones
+import java.util.Enumeration;
 import java.util.Hashtable;
-            berkley
+import java.util.ResourceBundle;
-            berkley
+import java.util.Random;
-            jones
+import java.util.PropertyResourceBundle;
-            jones
+import java.net.URL;
 import java.net.MalformedURLException;
-            jones
+import java.sql.PreparedStatement;
 import java.sql.ResultSet;
-            jones
+import java.sql.Connection;
-            jones
+import java.sql.SQLException;
-            berkley
+import java.lang.reflect.*;
-            berkley
+import java.net.*;
-            berkley
+import java.util.zip.*;
             jones
 import javax.servlet.ServletConfig;
 import javax.servlet.ServletContext;
 import javax.servlet.ServletException;
-            jones
+import javax.servlet.ServletInputStream;
-            jones
+import javax.servlet.http.HttpServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
-            bojilova
+import javax.servlet.http.HttpSession;
-            jones
+import javax.servlet.http.HttpUtils;
-            berkley
+import javax.servlet.ServletOutputStream;
             jones
-            jones
+import org.xml.sax.SAXException;
-            jones
+/**
  * A metadata catalog server implemented as a Java Servlet
             jones
  * <p>Valid parameters are:<br>
  * action=query -- query the values of all elements and attributes
  *                     and return a result set of nodes<br>
-            tao
+ * action=squery -- structured query (see pathquery.dtd)<br>
  * action= -- export a zip format for data packadge<br>
-            bojilova
+ * action=read -- read any metadata/data file from Metacat and from Internet<br>
-            jones
+ * action=insert -- insert an XML document into the database store<br>
  * action=update -- update an XML document that is in the database store<br>
  * action=delete --  delete an XML document from the database store<br>
  * action=validate -- vallidate the xml contained in valtext<br>
  * doctype -- document type list returned by the query (publicID)<br>
-            jones
+ * qformat=xml -- display resultset from query in XML<br>
  * qformat=html -- display resultset from query in HTML<br>
-            bojilova
+ * qformat=zip -- zip resultset from query<br>
-            jones
+ * docid=34 -- display the document with the document ID number 34<br>
-            jones
+ * doctext -- XML text of the document to load into the database<br>
-            bojilova
+ * acltext -- XML access text for a document to load into the database<br>
  * dtdtext -- XML DTD text for a new DTD to load into Metacat XML Catalog<br>
-            jones
+ * query -- actual query text (to go with 'action=query' or 'action=squery')<br>
-            jones
+ * valtext -- XML text to be validated<br>
-            bojilova
+ * abstractpath -- XPath in metadata document to read from<br>
-            bojilova
+ * action=getaccesscontrol -- retrieve acl info for Metacat document<br>
  * action=getdoctypes -- retrieve all doctypes (publicID)<br>
-            bojilova
+ * action=getdtdschema -- retrieve a DTD or Schema file<br>
-            bojilova
+ * action=getdataguide -- retrieve a Data Guide<br>
-            bojilova
+ * action=getprincipals -- retrieve a list of principals in XML<br>
-            jones
+ * datadoc -- data document name (id)<br>
  * <p>
  * The particular combination of parameters that are valid for each
  * particular action value is quite specific.  This documentation
  * will be reorganized to reflect this information.
-            jones
+ */
 public class MetaCatServlet extends HttpServlet {
-            berkley
+  private ServletConfig config = null;
   private ServletContext context = null;
   private String resultStyleURL = null;
   private String xmlcatalogfile = null;
   private String saxparser = null;
-            jones
+  private String datafilepath = null;
   private File dataDirectory = null;
-            berkley
+  private String servletpath = null;
-            jones
+  private String htmlpath = null;
-            jones
+  private PropertyResourceBundle options = null;
   private MetaCatUtil util = null;
-            tao
+  private DBConnectionPool connPool = null;
             jones
-            jones
+  /**
    * Initialize the servlet by creating appropriate database connections
    */
-            jones
+  public void init( ServletConfig config ) throws ServletException {
     try {
       super.init( config );
       this.config = config;
-            bojilova
+      this.context = config.getServletContext();
-            jones
+      System.out.println("MetaCatServlet Initialize");
             jones
-            jones
+      util = new MetaCatUtil();
             tao
       //initial DBConnection pool
       connPool = DBConnectionPool.getInstance();
             jones
-            jones
+      // Get the configuration file information
-            jones
+      resultStyleURL = util.getOption("resultStyleURL");
       xmlcatalogfile = util.getOption("xmlcatalogfile");
       saxparser = util.getOption("saxparser");
-            jones
+      datafilepath = util.getOption("datafilepath");
       dataDirectory = new File(datafilepath);
-            bojilova
+      servletpath = util.getOption("servletpath");
       htmlpath = util.getOption("htmlpath");
             bojilova
             tao
-            jones
+    } catch ( ServletException ex ) {
       throw ex;
-            tao
+    } catch (SQLException e) {
       MetaCatUtil.debugMessage("Error in MetacatServlet.init: "
                                           +e.getMessage(), 20);
             jones
+  }
-            bojilova
+  /**
    * Close all db connections from the pool
    */
   public void destroy() {
-            tao
+      // Close all db connection
       connPool.release();
             bojilova
-            jones
+  /** Handle "GET" method requests from HTTP clients */
-            jones
+  public void doGet (HttpServletRequest request, HttpServletResponse response)
     throws ServletException, IOException {
-            jones
+    // Process the data and send back the response
-            jones
+    handleGetOrPost(request, response);
             jones
-            jones
+  /** Handle "POST" method requests from HTTP clients */
-            jones
+  public void doPost( HttpServletRequest request, HttpServletResponse response)
     throws ServletException, IOException {
     // Process the data and send back the response
-            jones
+    handleGetOrPost(request, response);
             jones
-            jones
+  /**
-            jones
+   * Control servlet response depending on the action parameter specified
-            jones
+   */
-            berkley
+  private void handleGetOrPost(HttpServletRequest request,
-            jones
+                               HttpServletResponse response)
                                throws ServletException, IOException
+  {
             jones
-            bojilova
+    if ( util == null ) {
         util = new MetaCatUtil();
+    }
-            tao
+    /*MetaCatUtil.debugMessage("Connection pool size: "
-            tao
+                                     +connPool.getSizeOfDBConnectionPool(),10);
     MetaCatUtil.debugMessage("Free DBConnection number: "
-            tao
+                                  +connPool.getFreeDBConnectionNumber(), 10);*/
     //If all DBConnection in the pool are free and DBConnection pool
     //size is greater than initial value, shrink the connection pool
     //size to initial value
     DBConnectionPool.shrinkDBConnectionPoolSize();
-            tao
+    //Debug message to print out the method which have a busy DBConnection
     connPool.printMethodNameHavingBusyDBConnection();
-            jones
+    String ctype = request.getContentType();
     if (ctype != null && ctype.startsWith("multipart/form-data")) {
-            jones
+      handleMultipartForm(request, response);
     } else {
             tao
             jones
-            jones
+      String name = null;
       String[] value = null;
       String[] docid = new String[3];
       Hashtable params = new Hashtable();
       Enumeration paramlist = request.getParameterNames();
             tao
-            jones
+      while (paramlist.hasMoreElements()) {
             tao
-            jones
+        name = (String)paramlist.nextElement();
         value = request.getParameterValues(name);
         // Decode the docid and mouse click information
         if (name.endsWith(".y")) {
           docid[0] = name.substring(0,name.length()-2);
           params.put("docid", docid);
           name = "ypos";
             berkley
-            jones
+        if (name.endsWith(".x")) {
           name = "xpos";
+        }
         params.put(name,value);
             bojilova
             jones
             tao
       //handle param is emptpy
       if (params.isEmpty() || params == null)
+      {
         return;
+      }
-            jones
+      //if the user clicked on the input images, decode which image
       //was clicked then set the action.
       String action = ((String[])params.get("action"))[0];
-            tao
+      util.debugMessage("Line 230: Action is: " + action, 1);
             jones
       // This block handles session management for the servlet
       // by looking up the current session information for all actions
       // other than "login" and "logout"
       String username = null;
       String password = null;
-            bojilova
+      String[] groupnames = null;
-            jones
+      String sess_id = null;
       // handle login action
       if (action.equals("login")) {
-            tao
+        PrintWriter out = response.getWriter();
         handleLoginAction(out, params, request, response);
         out.close();
             jones
       // handle logout action
       } else if (action.equals("logout")) {
-            tao
+        PrintWriter out = response.getWriter();
         handleLogoutAction(out, params, request, response);
         out.close();
             tao
       // handle shrink DBConnection request
       } else if (action.equals("shrink")) {
         PrintWriter out = response.getWriter();
         boolean success = false;
         //If all DBConnection in the pool are free and DBConnection pool
         //size is greater than initial value, shrink the connection pool
         //size to initial value
         success = DBConnectionPool.shrinkConnectionPoolSize();
         if (success)
+        {
           //if successfully shrink the pool size to initial value
           out.println("DBConnection Pool shrink successfully");
         }//if
         else
+        {
           out.println("DBConnection pool couldn't shrink successfully");
+        }
        //close out put
         out.close();
-            jones
+      // aware of session expiration on every request
       } else {
         HttpSession sess = request.getSession(true);
         if (sess.isNew()) {
           // session expired or has not been stored b/w user requests
           username = "public";
           sess.setAttribute("username", username);
         } else {
           username = (String)sess.getAttribute("username");
           password = (String)sess.getAttribute("password");
-            bojilova
+          groupnames = (String[])sess.getAttribute("groupnames");
-            jones
+          try {
             sess_id = (String)sess.getId();
           } catch(IllegalStateException ise) {
             System.out.println("error in handleGetOrPost: this shouldn't " +
                                "happen: the session should be valid: " +
                                ise.getMessage());
+          }
+        }
+      }
-            tao
+       // Now that we know the session is valid, we can delegate the request
-            jones
+      // to a particular action handler
       if(action.equals("query")) {
-            tao
+        PrintWriter out = response.getWriter();
         handleQuery(out,params,response,username,groupnames);
         out.close();
-            jones
+      } else if(action.equals("squery")) {
-            tao
+        PrintWriter out = response.getWriter();
-            jones
+        if(params.containsKey("query")) {
-            tao
+         handleSQuery(out, params,response,username,groupnames);
          out.close();
-            jones
+        } else {
           out.println("Illegal action squery without \"query\" parameter");
-            tao
+          out.close();
             jones
-            tao
+      } else if (action.equals("export")) {
             tao
-            tao
+        handleExportAction(params, response, username, groupnames, password);
-            jones
+      } else if (action.equals("read")) {
-            tao
+        handleReadAction(params, response, username,password, groupnames);
-            jones
+      } else if (action.equals("insert") || action.equals("update")) {
-            berkley
+        PrintWriter out = response.getWriter();
-            jones
+        if ( (username != null) &&  !username.equals("public") ) {
-            bojilova
+          handleInsertOrUpdateAction(out,params,response,username,groupnames);
-            jones
+        } else {
           out.println("Permission denied for " + action);
             tao
         out.close();
-            jones
+      } else if (action.equals("delete")) {
         PrintWriter out = response.getWriter();
         if ( (username != null) &&  !username.equals("public") ) {
-            bojilova
+          handleDeleteAction(out, params, response, username, groupnames);
-            jones
+        } else {
           out.println("Permission denied for " + action);
             tao
         out.close();
-            jones
+      } else if (action.equals("validate")) {
         PrintWriter out = response.getWriter();
-            tao
+        handleValidateAction(out, params, response);
         out.close();
-            jones
+      } else if (action.equals("getaccesscontrol")) {
         PrintWriter out = response.getWriter();
-            bojilova
+        handleGetAccessControlAction(out,params,response,username,groupnames);
-            tao
+        out.close();
-            jones
+      } else if (action.equals("getprincipals")) {
         PrintWriter out = response.getWriter();
-            tao
+        handleGetPrincipalsAction(out, username, password);
         out.close();
-            jones
+      } else if (action.equals("getdoctypes")) {
         PrintWriter out = response.getWriter();
-            tao
+        handleGetDoctypesAction(out, params, response);
         out.close();
-            jones
+      } else if (action.equals("getdtdschema")) {
         PrintWriter out = response.getWriter();
-            tao
+        handleGetDTDSchemaAction(out, params, response);
         out.close();
-            jones
+      } else if (action.equals("getdataguide")) {
         PrintWriter out = response.getWriter();
-            tao
+        handleGetDataGuideAction(out, params, response);
         out.close();
-            jones
+      } else if (action.equals("getlastdocid")) {
         PrintWriter out = response.getWriter();
-            tao
+        handleGetMaxDocidAction(out, params, response);
         out.close();
-            tao
+      } else if (action.equals("getrevisionanddoctype")) {
         PrintWriter out = response.getWriter();
         handleGetRevisionAndDocTypeAction(out, params);
         out.close();
-            jones
+      } else if (action.equals("login") || action.equals("logout")) {
       } else if (action.equals("protocoltest")) {
         String testURL = "metacat://dev.nceas.ucsb.edu/NCEAS.897766.9";
         try {
           testURL = ((String[])params.get("url"))[0];
         } catch (Throwable t) {
+        }
         String phandler = System.getProperty("java.protocol.handler.pkgs");
         response.setContentType("text/html");
         PrintWriter out = response.getWriter();
         out.println("<body bgcolor=\"white\">");
         out.println("<p>Handler property: <code>" + phandler + "</code></p>");
         out.println("<p>Starting test for:<br>");
         out.println("    " + testURL + "</p>");
         try {
           URL u = new URL(testURL);
           out.println("<pre>");
           out.println("Protocol: " + u.getProtocol());
           out.println("    Host: " + u.getHost());
           out.println("    Port: " + u.getPort());
           out.println("    Path: " + u.getPath());
           out.println("     Ref: " + u.getRef());
           String pquery = u.getQuery();
           out.println("   Query: " + pquery);
           out.println("  Params: ");
           if (pquery != null) {
             Hashtable qparams = util.parseQuery(u.getQuery());
             for (Enumeration en = qparams.keys(); en.hasMoreElements(); ) {
               String pname = (String)en.nextElement();
               String pvalue = (String)qparams.get(pname);
               out.println("    " + pname + ": " + pvalue);
+            }
             jones
-            jones
+          out.println("</pre>");
           out.println("</body>");
           out.close();
         } catch (MalformedURLException mue) {
           System.out.println("bad url from MetacatServlet.handleGetOrPost");
           out.println(mue.getMessage());
           mue.printStackTrace(out);
           out.close();
             jones
-            jones
+      } else {
         PrintWriter out = response.getWriter();
         out.println("<?xml version=\"1.0\"?>");
         out.println("<error>");
         out.println("Error: action not registered.  Please report this error.");
         out.println("</error>");
-            tao
+        out.close();
             jones
             jones
-            tao
+      //util.closeConnections();
-            jones
+      // Close the stream to the client
-            tao
+      //out.close();
             jones
+  }
             berkley
-            bojilova
+  // LOGIN & LOGOUT SECTION
-            jones
+  /**
-            bojilova
+   * Handle the login request. Create a new session object.
-            bojilova
+   * Do user authentication through the session.
-            bojilova
+   */
   private void handleLoginAction(PrintWriter out, Hashtable params,
                HttpServletRequest request, HttpServletResponse response) {
             bojilova
-            bojilova
+    AuthSession sess = null;
-            bojilova
+    String un = ((String[])params.get("username"))[0];
     String pw = ((String[])params.get("password"))[0];
-            bojilova
+    String action = ((String[])params.get("action"))[0];
-            bojilova
+    String qformat = ((String[])params.get("qformat"))[0];
             bojilova
-            bojilova
+    try {
-            bojilova
+      sess = new AuthSession();
-            bojilova
+    } catch (Exception e) {
-            berkley
+      System.out.println("error in MetacatServlet.handleLoginAction: " +
                           e.getMessage());
-            bojilova
+      out.println(e.getMessage());
-            bojilova
+      return;
             bojilova
-            bojilova
+    boolean isValid = sess.authenticate(request, un, pw);
     // format and transform the output
-            jones
+    if (qformat.equals("xml")) {
       response.setContentType("text/xml");
       out.println(sess.getMessage());
     } else {
             tao
-            bojilova
+      try {
             tao
         DBTransform trans = new DBTransform();
-            bojilova
+        response.setContentType("text/html");
-            bojilova
+        trans.transformXMLDocument(sess.getMessage(), "-//NCEAS//login//EN",
-            jones
+                                   "-//W3C//HTML//EN", qformat, out);
             tao
-            bojilova
+      } catch(Exception e) {
             tao
         MetaCatUtil.debugMessage("Error in MetaCatServlet.handleLoginAction: "
                                 +e.getMessage(), 30);
             bojilova
     // any output is returned
             bojilova
             berkley
             bojilova
   /**
    * Handle the logout request. Close the connection.
    */
   private void handleLogoutAction(PrintWriter out, Hashtable params,
                HttpServletRequest request, HttpServletResponse response) {
     String qformat = ((String[])params.get("qformat"))[0];
     // close the connection
     HttpSession sess = request.getSession(false);
     if (sess != null) { sess.invalidate();  }
     // produce output
     StringBuffer output = new StringBuffer();
     output.append("<?xml version=\"1.0\"?>");
-            bojilova
+    output.append("<logout>");
     output.append("User logged out");
     output.append("</logout>");
             bojilova
     //format and transform the output
-            jones
+    if (qformat.equals("xml")) {
       response.setContentType("text/xml");
       out.println(output.toString());
     } else {
             tao
-            bojilova
+      try {
             tao
         DBTransform trans = new DBTransform();
-            bojilova
+        response.setContentType("text/html");
-            bojilova
+        trans.transformXMLDocument(output.toString(), "-//NCEAS//login//EN",
-            jones
+                                   "-//W3C//HTML//EN", qformat, out);
             tao
-            bojilova
+      } catch(Exception e) {
             tao
         MetaCatUtil.debugMessage("Error in MetaCatServlet.handleLogoutAction"
                                   +e.getMessage(), 30);
             bojilova
+    }
+  }
-            bojilova
+  // END OF LOGIN & LOGOUT SECTION
             berkley
-            bojilova
+  // SQUERY & QUERY SECTION
-            berkley
+  /**
-            jones
+   * Retreive the squery xml, execute it and display it
+   *
    * @param out the output stream to the client
    * @param params the Hashtable of parameters that should be included
    * in the squery.
    * @param response the response object linked to the client
    * @param conn the database connection
    */
   protected void handleSQuery(PrintWriter out, Hashtable params,
-            bojilova
+                 HttpServletResponse response, String user, String[] groups)
             berkley
-            jones
+    String xmlquery = ((String[])params.get("query"))[0];
     String qformat = ((String[])params.get("qformat"))[0];
-            berkley
+    String resultdoc = null;
-            tao
+    MetaCatUtil.debugMessage("xmlquery: "+xmlquery, 30);
     double startTime = System.currentTimeMillis()/1000;
-            bojilova
+    Hashtable doclist = runQuery(xmlquery, user, groups);
-            tao
+    double docListTime = System.currentTimeMillis()/1000;
     MetaCatUtil.debugMessage("Time for getting doc list: "
                                             +(docListTime-startTime), 30);
-            berkley
+    resultdoc = createResultDocument(doclist, transformQuery(xmlquery));
-            tao
+    double toStringTime = System.currentTimeMillis()/1000;
     MetaCatUtil.debugMessage("Time to create xml string: "
                               +(toStringTime-docListTime), 30);
     //format and transform the results
     double outPutTime = 0;
-            jones
+    if(qformat.equals("xml")) {
-            jones
+      response.setContentType("text/xml");
       out.println(resultdoc);
-            tao
+      outPutTime = System.currentTimeMillis()/1000;
       MetaCatUtil.debugMessage("Output time: "+(outPutTime-toStringTime), 30);
-            jones
+    } else {
-            jones
+      transformResultset(resultdoc, response, out, qformat);
-            tao
+      outPutTime = System.currentTimeMillis()/1000;
       MetaCatUtil.debugMessage("Output time: "+(outPutTime-toStringTime), 30);
             jones
             berkley
             tao
-            berkley
+   /**
-            jones
+    * Create the xml query, execute it and display the results.
+    *
     * @param out the output stream to the client
     * @param params the Hashtable of parameters that should be included
-            berkley
+    * in the squery.
-            jones
+    * @param response the response object linked to the client
-            berkley
+    */
-            berkley
+  protected void handleQuery(PrintWriter out, Hashtable params,
-            bojilova
+                 HttpServletResponse response, String user, String[] groups)
             berkley
-            berkley
+    //create the query and run it
-            berkley
+    String xmlquery = DBQuery.createSQuery(params);
-            bojilova
+    Hashtable doclist = runQuery(xmlquery, user, groups);
-            berkley
+    String qformat = ((String[])params.get("qformat"))[0];
     String resultdoc = null;
     resultdoc = createResultDocument(doclist, transformQuery(params));
             bojilova
-            berkley
+    //format and transform the results
-            jones
+    if(qformat.equals("xml")) {
-            berkley
+      response.setContentType("text/xml");
       out.println(resultdoc);
-            berkley
+    } else {
-            jones
+      transformResultset(resultdoc, response, out, qformat);
             berkley
             berkley
   /**
-            berkley
+   * Removes the <?xml version="x"?> tag from the beginning of xmlquery
    * so it can properly be placed in the <query> tag of the resultset.
    * This method is overwritable so that other applications can customize
    * the structure of what is in the <query> tag.
+   *
    * @param xmlquery is the query to remove the <?xml version="x"?> tag from.
    */
   protected String transformQuery(Hashtable params)
+  {
     //DBQuery.createSQuery is a re-calling of a previously called
     //function but it is necessary
     //so that overriding methods have access to the params hashtable
     String xmlquery = DBQuery.createSQuery(params);
     //the <?xml version="1.0"?> tag is the first 22 characters of the
     xmlquery = xmlquery.trim();
     int index = xmlquery.indexOf("?>");
     return xmlquery.substring(index + 2, xmlquery.length());
+  }
   /**
-            berkley
+   * removes the <?xml version="1.0"?> tag from the beginning.  This takes a
    * string as a param instead of a hashtable.
+   *
    * @param xmlquery a string representing a query.
    */
   protected String transformQuery(String xmlquery)
+  {
     xmlquery = xmlquery.trim();
     int index = xmlquery.indexOf("?>");
     return xmlquery.substring(index + 2, xmlquery.length());
+  }
   /**
-            jones
+   * Run the query and return a hashtable of results.
+   *
    * @param xmlquery the query to run
    */
-            bojilova
+  private Hashtable runQuery(String xmlquery, String user, String[] groups)
             berkley
     Hashtable doclist=null;
             tao
-            berkley
+    try
+    {
             tao
       DBQuery queryobj = new DBQuery(saxparser);
-            bojilova
+      doclist = queryobj.findDocuments(new StringReader(xmlquery),user,groups);
             tao
-            bojilova
+      return doclist;
             berkley
     catch (Exception e)
+    {
             tao
       MetaCatUtil.debugMessage("Error in MetacatServlet.runQuery: "
                                                       + e.getMessage(), 30);
-            berkley
+      doclist = null;
       return doclist;
+    }
+  }
-            jones
+  /**
-            berkley
+   * Transorms an xml resultset document to html and sends it to the browser
             jones
-            berkley
+   * @param resultdoc the string representation of the document that needs
    * to be transformed.
    * @param response the HttpServletResponse object bound to the client.
    * @param out the output stream to the client
-            jones
+   * @param qformat the name of the style-set to use for transformations
-            berkley
+   */
   protected void transformResultset(String resultdoc,
-            jones
+                                    HttpServletResponse response,
-            jones
+                                    PrintWriter out, String qformat)
             berkley
             tao
-            jones
+    try {
             tao
       DBTransform trans = new DBTransform();
-            berkley
+      response.setContentType("text/html");
       trans.transformXMLDocument(resultdoc, "-//NCEAS//resultset//EN",
-            jones
+                                 "-//W3C//HTML//EN", qformat, out);
             tao
             berkley
     catch(Exception e)
+    {
             tao
       MetaCatUtil.debugMessage("Error in MetaCatServlet.transformResultset:"
                                 +e.getMessage(), 30);
             berkley
+  }
-            berkley
+  /**
    * Transforms a hashtable of documents to an xml or html result.
             jones
-            berkley
+   * @param doclist- the hashtable to transform
-            jones
+   * @param xmlquery- the query that returned the doclist result
-            berkley
+   */
-            berkley
+  protected String createResultDocument(Hashtable doclist, String xmlquery)
             berkley
     // Create a buffer to hold the xml result
     StringBuffer resultset = new StringBuffer();
-            berkley
+    // Print the resulting root nodes
-            berkley
+    String docid = null;
     String document = null;
     resultset.append("<?xml version=\"1.0\"?>\n");
     resultset.append("<resultset>\n");
             berkley
-            berkley
+    resultset.append("  <query>" + xmlquery + "</query>");
             berkley
     if(doclist != null)
             berkley
-            berkley
+      Enumeration doclistkeys = doclist.keys();
       while (doclistkeys.hasMoreElements())
+      {
         docid = (String)doclistkeys.nextElement();
         document = (String)doclist.get(docid);
         resultset.append("  <document>" + document + "</document>");
+      }
+    }
-            berkley
+    resultset.append("</resultset>");
-            berkley
+    return resultset.toString();
             berkley
-            bojilova
+  // END OF SQUERY & QUERY SECTION
             berkley
-            tao
+ //Exoport section
  /**
    * Handle the "export" request of data package from Metacat in zip format
    * @param params the Hashtable of HTTP request parameters
    * @param response the HTTP response object linked to the client
    * @param user the username sent the request
    * @param groups the user's groupnames
    */
-            tao
+  private void handleExportAction(Hashtable params,
     HttpServletResponse response, String user, String[] groups, String passWord)
             tao
-            tao
+    // Output stream
-            tao
+    ServletOutputStream out = null;
-            tao
+    // Zip output stream
-            tao
+    ZipOutputStream zOut = null;
     DocumentImpl docImpls=null;
     DBQuery queryObj=null;
             tao
-            tao
+    String[] docs = new String[10];
     String docId = "";
     try
+    {
       // read the params
-            tao
+      if (params.containsKey("docid"))
+      {
-            tao
+        docs = (String[])params.get("docid");
-            tao
+      }//if
       // Create a DBuery to handle export
       queryObj = new DBQuery(saxparser);
       // Get the docid
-            tao
+      docId=docs[0];
-            tao
+      // Make sure the client specify docid
       if (docId == null || docId.equals(""))
+      {
         response.setContentType("text/xml"); //MIME type
         // Get a printwriter
         PrintWriter pw = response.getWriter();
         // Send back message
         pw.println("<?xml version=\"1.0\"?>");
         pw.println("<error>");
         pw.println("You didn't specify requested docid");
         pw.println("</error>");
         // Close printwriter
         pw.close();
         return;
       }//if
       // Get output stream
-            tao
+      out = response.getOutputStream();
       response.setContentType("application/zip"); //MIME type
       zOut = new ZipOutputStream(out);
-            tao
+      zOut =queryObj.getZippedPackage(docId, out, user, groups, passWord);
-            tao
+      zOut.finish(); //terminate the zip file
       zOut.close();  //close the zip stream
             tao
-            tao
+    }//try
-            tao
+    catch (Exception e)
+    {
       try
+      {
         response.setContentType("text/xml"); //MIME type
-            tao
+        // Send error message back
-            tao
+        if (out != null)
+        {
             PrintWriter pw = new PrintWriter(out);
             pw.println("<?xml version=\"1.0\"?>");
             pw.println("<error>");
             pw.println(e.getMessage());
             pw.println("</error>");
-            tao
+            // Close printwriter
-            tao
+            pw.close();
-            tao
+            // Close output stream
             out.close();
         }//if
         // Close zip output stream
-            tao
+        if ( zOut != null )
+        {
           zOut.close();
-            tao
+        }//if
       }//try
-            tao
+      catch (IOException ioe)
+      {
-            tao
+        MetaCatUtil.debugMessage("Problem with the servlet output " +
-            tao
+                           "in MetacatServlet.handleExportAction: " +
-            tao
+                           ioe.getMessage(), 30);
-            tao
+      }//catch
             tao
-            tao
+      MetaCatUtil.debugMessage("Error in MetacatServlet.handleExportAction: " +
-            tao
+                         e.getMessage(), 30);
-            tao
+      e.printStackTrace(System.out);
             tao
     }//catch
             tao
-            tao
+  }//handleExportAction
-            bojilova
+  // READ SECTION
   /**
    * Handle the "read" request of metadata/data files from Metacat
    * or any files from Internet;
    * transformed metadata XML document into HTML presentation if requested;
    * zip files when more than one were requested.
+   *
    * @param params the Hashtable of HTTP request parameters
    * @param response the HTTP response object linked to the client
    * @param user the username sent the request
-            bojilova
+   * @param groups the user's groupnames
-            berkley
+   */
-            bojilova
+  private void handleReadAction(Hashtable params, HttpServletResponse response,
-            tao
+                                String user, String passWord, String[] groups)
             berkley
-            bojilova
+    ServletOutputStream out = null;
     ZipOutputStream zout = null;
-            tao
+    PrintWriter pw = null;
     boolean zip = false;
             bojilova
     try {
       String[] docs = new String[0];
       String docid = "";
       String qformat = "";
       String abstrpath = null;
             tao
-            bojilova
+      // read the params
       if (params.containsKey("docid")) {
         docs = (String[])params.get("docid");
             berkley
-            bojilova
+      if (params.containsKey("qformat")) {
         qformat = ((String[])params.get("qformat"))[0];
             berkley
-            bojilova
+      if (params.containsKey("abstractpath")) {
         abstrpath = ((String[])params.get("abstractpath"))[0];
-            bojilova
+        if ( !abstrpath.equals("") && (abstrpath != null) ) {
           viewAbstract(response, abstrpath, docs[0]);
           return;
+        }
             berkley
-            bojilova
+      if ( (docs.length > 1) || qformat.equals("zip") ) {
         zip = true;
         out = response.getOutputStream();
         response.setContentType("application/zip"); //MIME type
         zout = new ZipOutputStream(out);
+      }
       // go through the list of docs to read
       for (int i=0; i < docs.length; i++ ) {
         try {
           URL murl = new URL(docs[i]);
           Hashtable murlQueryStr = util.parseQuery(murl.getQuery());
           // case docid="http://.../?docid=aaa"
           // or docid="metacat://.../?docid=bbb"
           if (murlQueryStr.containsKey("docid")) {
             // get only docid, eliminate the rest
             docid = (String)murlQueryStr.get("docid");
             if ( zip ) {
-            tao
+              addDocToZip(docid, zout, user, groups);
-            bojilova
+            } else {
               readFromMetacat(response, docid, qformat, abstrpath,
-            bojilova
+                              user, groups, zip, zout);
             bojilova
           // case docid="http://.../filename"
           } else {
             docid = docs[i];
             if ( zip ) {
-            tao
+              addDocToZip(docid, zout, user, groups);
-            bojilova
+            } else {
               readFromURLConnection(response, docid);
+            }
+          }
         // case docid="ccc"
         } catch (MalformedURLException mue) {
           docid = docs[i];
           if ( zip ) {
-            tao
+            addDocToZip(docid, zout, user, groups);
-            bojilova
+          } else {
             readFromMetacat(response, docid, qformat, abstrpath,
-            bojilova
+                            user, groups, zip, zout);
             bojilova
+        }
       } /* end for */
       if ( zip ) {
         zout.finish(); //terminate the zip file
         zout.close();  //close the zip stream
+      }
             tao
             tao
     // To handle doc not found exception
     catch (McdbDocNotFoundException notFoundE)
+    {
       // the docid which didn't be found
       String notFoundDocId = notFoundE.getUnfoundDocId();
       String notFoundRevision = notFoundE.getUnfoundRevision();
       MetaCatUtil.debugMessage("Missed id: "+ notFoundDocId, 30);
       MetaCatUtil.debugMessage("Missed rev: "+ notFoundRevision, 30);
       try
+      {
         // read docid from remote server
         readFromRemoteMetaCat(response, notFoundDocId, notFoundRevision,
                                               user, passWord, out, zip, zout);
         // Close zout outputstream
         if ( zout != null)
+        {
           zout.close();
+        }
         // close output stream
         if (out != null)
+        {
           out.close();
+        }
       }//try
       catch ( Exception exc)
+      {
         MetaCatUtil.debugMessage("Erorr in MetacatServlet.hanldReadAction: "+
                                       exc.getMessage(), 30);
         try
+        {
           if (out != null)
+          {
             response.setContentType("text/xml");
             // Send back error message by printWriter
             pw = new PrintWriter(out);
             pw.println("<?xml version=\"1.0\"?>");
             pw.println("<error>");
             pw.println(notFoundE.getMessage());
             pw.println("</error>");
             pw.close();
             out.close();
+          }
           else
+          {
            response.setContentType("text/xml"); //MIME type
            // Send back error message if out = null
            if (pw == null)
+           {
              // If pw is null, open the respnose
             pw = response.getWriter();
+           }
            pw.println("<?xml version=\"1.0\"?>");
            pw.println("<error>");
            pw.println(notFoundE.getMessage());
            pw.println("</error>");
            pw.close();
+        }
         // close zout
         if ( zout != null )
+        {
           zout.close();
+        }
         }//try
         catch (IOException ie)
+        {
           MetaCatUtil.debugMessage("Problem with the servlet output " +
                            "in MetacatServlet.handleReadAction: " +
                            ie.getMessage(), 30);
         }//cathch
       }//catch
     }// catch McdbDocNotFoundException
     catch (Exception e)
+    {
-            bojilova
+      try {
             tao
-            jones
+        if (out != null) {
-            tao
+            response.setContentType("text/xml"); //MIME type
             pw = new PrintWriter(out);
-            jones
+            pw.println("<?xml version=\"1.0\"?>");
             pw.println("<error>");
             pw.println(e.getMessage());
             pw.println("</error>");
             pw.close();
-            tao
+            out.close();
             jones
-            tao
+        else
+        {
            response.setContentType("text/xml"); //MIME type
            // Send back error message if out = null
            if ( pw == null)
+           {
             pw = response.getWriter();
+           }
            pw.println("<?xml version=\"1.0\"?>");
            pw.println("<error>");
            pw.println(e.getMessage());
            pw.println("</error>");
            pw.close();
+        }
         // Close zip output stream
-            bojilova
+        if ( zout != null ) { zout.close(); }
             tao
-            bojilova
+      } catch (IOException ioe) {
-            tao
+        MetaCatUtil.debugMessage("Problem with the servlet output " +
-            bojilova
+                           "in MetacatServlet.handleReadAction: " +
-            tao
+                           ioe.getMessage(), 30);
-            bojilova
+        ioe.printStackTrace(System.out);
+      }
       System.out.println("Error in MetacatServlet.handleReadAction: " +
-            berkley
+                         e.getMessage());
-            bojilova
+      e.printStackTrace(System.out);
             berkley
+  }
             bojilova
   // read metadata or data from Metacat
   private void readFromMetacat(HttpServletResponse response, String docid,
                                String qformat, String abstrpath, String user,
-            tao
+                             String[] groups, boolean zip, ZipOutputStream zout)
-            bojilova
+               throws ClassNotFoundException, IOException, SQLException,
                       McdbException, Exception
             berkley
             tao
-            bojilova
+    try {
             tao
             berkley
-            tao
+      DocumentImpl doc = new DocumentImpl(docid);
-            tao
+      //check the permission for read
-            tao
+      if (!doc.hasReadPermission(user, groups, docid))
             tao
         Exception e = new Exception("User " + user + " does not have permission"
                        +" to read the document with the docid " + docid);
             tao
-            tao
+        throw e;
+      }
-            bojilova
+      if ( doc.getRootNodeID() == 0 ) {
         // this is data file
         String filepath = util.getOption("datafilepath");
         if(!filepath.endsWith("/")) {
           filepath += "/";
+        }
-            tao
+        String filename = filepath + docid;
         FileInputStream fin = null;
         fin = new FileInputStream(filename);
         //MIME type
-            bojilova
+        String contentType = getServletContext().getMimeType(filename);
         if (contentType == null) {
           if (filename.endsWith(".xml")) {
             contentType="text/xml";
           } else if (filename.endsWith(".css")) {
             contentType="text/css";
           } else if (filename.endsWith(".dtd")) {
             contentType="text/plain";
           } else if (filename.endsWith(".xsd")) {
-            bojilova
+            contentType="text/xml";
-            bojilova
+          } else if (filename.endsWith("/")) {
-            bojilova
+            contentType="text/html";
-            bojilova
+          } else {
-            bojilova
+            File f = new File(filename);
             if ( f.isDirectory() ) {
               contentType="text/html";
             } else {
               contentType="application/octet-stream";
+            }
             berkley
+        }
-            bojilova
+        response.setContentType(contentType);
-            bojilova
+        // if we decide to use "application/octet-stream" for all data returns
         // response.setContentType("application/octet-stream");
             tao
-            bojilova
+        try {
             tao
           ServletOutputStream out = response.getOutputStream();
-            bojilova
+          byte[] buf = new byte[4 * 1024]; // 4K buffer
           int b = fin.read(buf);
           while (b != -1) {
             out.write(buf, 0, b);
             b = fin.read(buf);
             berkley
-            bojilova
+        } finally {
           if (fin != null) fin.close();
             berkley
             bojilova
       } else {
         // this is metadata doc
-            jones
+        if ( qformat.equals("xml") ) {
             tao
-            jones
+          // set content type first
           response.setContentType("text/xml");   //MIME type
           PrintWriter out = response.getWriter();
           doc.toXml(out);
         } else {
-            bojilova
+          response.setContentType("text/html");  //MIME type
           PrintWriter out = response.getWriter();
           // Look up the document type
           String doctype = doc.getDoctype();
           // Transform the document to the new doctype
-            tao
+          DBTransform dbt = new DBTransform();
-            bojilova
+          dbt.transformXMLDocument(doc.toString(),
-            jones
+                                   doctype,"-//W3C//HTML//EN", qformat, out);
             bojilova
             berkley
             tao
     catch (Exception except)
+    {
-            tao
+      throw except;
             bojilova
+  }
             berkley
-            bojilova
+  // read data from URLConnection
   private void readFromURLConnection(HttpServletResponse response, String docid)
                throws IOException, MalformedURLException
             jones
-            bojilova
+    ServletOutputStream out = response.getOutputStream();
     String contentType = getServletContext().getMimeType(docid); //MIME type
     if (contentType == null) {
       if (docid.endsWith(".xml")) {
         contentType="text/xml";
       } else if (docid.endsWith(".css")) {
         contentType="text/css";
       } else if (docid.endsWith(".dtd")) {
         contentType="text/plain";
       } else if (docid.endsWith(".xsd")) {
-            bojilova
+        contentType="text/xml";
-            bojilova
+      } else if (docid.endsWith("/")) {
-            bojilova
+        contentType="text/html";
-            bojilova
+      } else {
-            bojilova
+        File f = new File(docid);
         if ( f.isDirectory() ) {
           contentType="text/html";
         } else {
           contentType="application/octet-stream";
+        }
             bojilova
+    }
     response.setContentType(contentType);
-            bojilova
+    // if we decide to use "application/octet-stream" for all data returns
     // response.setContentType("application/octet-stream");
             bojilova
     // this is http url
     URL url = new URL(docid);
     BufferedInputStream bis = null;
-            jones
+    try {
-            bojilova
+      bis = new BufferedInputStream(url.openStream());
       byte[] buf = new byte[4 * 1024]; // 4K buffer
       int b = bis.read(buf);
       while (b != -1) {
         out.write(buf, 0, b);
         b = bis.read(buf);
             berkley
-            bojilova
+    } finally {
       if (bis != null) bis.close();
             jones
             bojilova
             jones
             berkley
-            bojilova
+  // read file/doc and write to ZipOutputStream
-            tao
+  private void addDocToZip(String docid, ZipOutputStream zout,
                               String user, String[] groups)
-            bojilova
+               throws ClassNotFoundException, IOException, SQLException,
                       McdbException, Exception
             berkley
-            bojilova
+    byte[] bytestring = null;
     ZipEntry zentry = null;
     try {
       URL url = new URL(docid);
       // this http url; read from URLConnection; add to zip
       zentry = new ZipEntry(docid);
       zout.putNextEntry(zentry);
       BufferedInputStream bis = null;
       try {
         bis = new BufferedInputStream(url.openStream());
         byte[] buf = new byte[4 * 1024]; // 4K buffer
         int b = bis.read(buf);
         while(b != -1) {
           zout.write(buf, 0, b);
           b = bis.read(buf);
+        }
       } finally {
         if (bis != null) bis.close();
             berkley
-            bojilova
+      zout.closeEntry();
     } catch (MalformedURLException mue) {
             berkley
-            bojilova
+      // this is metacat doc (data file or metadata doc)
             tao
-            bojilova
+      try {
             tao
         DocumentImpl doc = new DocumentImpl(docid);
             tao
         //check the permission for read
-            tao
+        if (!doc.hasReadPermission(user, groups, docid))
             tao
           Exception e = new Exception("User " + user + " does not have "
                     +"permission to read the document with the docid " + docid);
             tao
-            tao
+          throw e;
+        }
-            bojilova
+        if ( doc.getRootNodeID() == 0 ) {
           // this is data file; add file to zip
           String filepath = util.getOption("datafilepath");
           if(!filepath.endsWith("/")) {
             filepath += "/";
+          }
-            tao
+          String filename = filepath + docid;
-            bojilova
+          FileInputStream fin = null;
-            tao
+          fin = new FileInputStream(filename);
-            bojilova
+          try {
             tao
             zentry = new ZipEntry(docid);
             zout.putNextEntry(zentry);
-            bojilova
+            byte[] buf = new byte[4 * 1024]; // 4K buffer
             int b = fin.read(buf);
             while (b != -1) {
               zout.write(buf, 0, b);
               b = fin.read(buf);
+            }
           } finally {
             if (fin != null) fin.close();
+          }
           zout.closeEntry();
         } else {
           // this is metadata doc; add doc to zip
           bytestring = doc.toString().getBytes();
           zentry = new ZipEntry(docid + ".xml");
           zentry.setSize(bytestring.length);
           zout.putNextEntry(zentry);
           zout.write(bytestring, 0, bytestring.length);
           zout.closeEntry();
             berkley
-            tao
+      } catch (Exception except) {
         throw except;
             berkley
+    }
             bojilova
             berkley
             bojilova
   // view abstract within document
   private void viewAbstract(HttpServletResponse response,
                             String abstractpath, String docid)
                throws ClassNotFoundException, IOException, SQLException,
                       McdbException, Exception
+  {
             tao
     PrintWriter out =null;
-            jones
+    try {
             tao
-            bojilova
+      response.setContentType("text/html");  //MIME type
-            tao
+      out = response.getWriter();
       Object[] abstracts = DBQuery.getNodeContent(abstractpath, docid);
-            bojilova
+      out.println("<html><head><title>Abstract</title></head>");
       out.println("<body bgcolor=\"white\"><h1>Abstract</h1>");
       for (int i=0; i<abstracts.length; i++) {
         out.println("<p>" + (String)abstracts[i] + "</p>");
+      }
       out.println("</body></html>");
             jones
-            tao
+    } catch (Exception e) {
        out.println("<?xml version=\"1.0\"?>");
        out.println("<error>");
        out.println(e.getMessage());
        out.println("</error>");
             bojilova
             jones
-            tao
+  /**
    * If metacat couldn't find a data file or document locally, it will read this
    * docid from its home server. This is for the replication feature
    */
   private void readFromRemoteMetaCat(HttpServletResponse response, String docid,
                      String rev, String user, String password,
                      ServletOutputStream out, boolean zip, ZipOutputStream zout)
                         throws Exception
+ {
    // Create a object of RemoteDocument, "" is for zipEntryPath
    RemoteDocument remoteDoc =
                         new RemoteDocument (docid, rev,user, password, "");
-            tao
+   String docType = remoteDoc.getDocType();
    // Only read data file
    if (docType.equals("BIN"))
             tao
-            tao
+    // If it is zip format
     if (zip)
+    {
       remoteDoc.readDocumentFromRemoteServerByZip(zout);
     }//if
     else
+    {
       if (out == null)
+      {
         out = response.getOutputStream();
       }//if
       response.setContentType("application/octet-stream");
       remoteDoc.readDocumentFromRemoteServer(out);
     }//else (not zip)
    }//if doctype=bin
-            tao
+   else
+   {
-            tao
+     throw new Exception("Docid: "+docid+"."+rev+" couldn't find");
    }//else
-            tao
+ }//readFromRemoteMetaCat
-            bojilova
+  // END OF READ SECTION
   // INSERT/UPDATE SECTION
-            jones
+  /**
    * Handle the database putdocument request and write an XML document
    * to the database connection
    */
-            berkley
+  private void handleInsertOrUpdateAction(PrintWriter out, Hashtable params,
-            bojilova
+               HttpServletResponse response, String user, String[] groups) {
             jones
-            tao
+    DBConnection dbConn = null;
     int serialNumber = -1;
             bojilova
-            jones
+    try {
       // Get the document indicated
       String[] doctext = (String[])params.get("doctext");
             bojilova
-            bojilova
+      String pub = null;
       if (params.containsKey("public")) {
         pub = ((String[])params.get("public"))[0];
             bojilova
             bojilova
-            bojilova
+      StringReader dtd = null;
-            bojilova
+      if (params.containsKey("dtdtext")) {
-            bojilova
+        String[] dtdtext = (String[])params.get("dtdtext");
         try {
-            bojilova
+          if ( !dtdtext[0].equals("") ) {
             dtd = new StringReader(dtdtext[0]);
+          }
-            bojilova
+        } catch (NullPointerException npe) {}
+      }
             bojilova
-            jones
+      StringReader xml = null;
-            bojilova
+      boolean validate = false;
-            jones
+      try {
-            bojilova
+        // look inside XML Document for <!DOCTYPE ... PUBLIC/SYSTEM ... >
         // in order to decide whether to use validation parser
         validate = validateXML(doctext[0]);
-            jones
+        xml = new StringReader(doctext[0]);
             jones
-            jones
+        String[] action = (String[])params.get("action");
         String[] docid = (String[])params.get("docid");
         String newdocid = null;
             jones
-            jones
+        String doAction = null;
         if (action[0].equals("insert")) {
           doAction = "INSERT";
         } else if (action[0].equals("update")) {
           doAction = "UPDATE";
+        }
             tao
         try
+        {
-            bojilova
+          // get a connection from the pool
-            tao
+          dbConn=DBConnectionPool.
                   getDBConnection("MetaCatServlet.handleInsertOrUpdateAction");
           serialNumber=dbConn.getCheckOutSerialNumber();
             tao
-            bojilova
+          // write the document to the database
-            tao
+          try
+          {
-            bojilova
+            String accNumber = docid[0];
-            tao
+            MetaCatUtil.debugMessage(""+ doAction + " " + accNumber +"...", 10);
-            tao
+            if (accNumber.equals(""))
+            {
-            bojilova
+              accNumber = null;
-            tao
+            }//if
             newdocid = DocumentImpl.write(dbConn, xml, pub, dtd, doAction,
-            bojilova
+                                          accNumber, user, groups, validate);
             tao
           }//try
           catch (NullPointerException npe)
+          {
             newdocid = DocumentImpl.write(dbConn, xml, pub, dtd, doAction,
-            bojilova
+                                          null, user, groups, validate);
-            tao
+          }//catch
         }//try
         finally
+        {
           // Return db connection
           DBConnectionPool.returnDBConnection(dbConn, serialNumber);
             bojilova
-            jones
+        // set content type and other response header fields first
         response.setContentType("text/xml");
         out.println("<?xml version=\"1.0\"?>");
         out.println("<success>");
         out.println("<docid>" + newdocid + "</docid>");
         out.println("</success>");
-            jones
+      } catch (NullPointerException npe) {
-            jones
+        response.setContentType("text/xml");
         out.println("<?xml version=\"1.0\"?>");
         out.println("<error>");
         out.println(npe.getMessage());
         out.println("</error>");
             jones
-            jones
+    } catch (Exception e) {
       response.setContentType("text/xml");
       out.println("<?xml version=\"1.0\"?>");
       out.println("<error>");
       out.println(e.getMessage());
       if (e instanceof SAXException) {
         Exception e2 = ((SAXException)e).getException();
         out.println("<error>");
-            berkley
+        try
+        {
           out.println(e2.getMessage());
+        }
         catch(NullPointerException npe)
+        {
           out.println(e.getMessage());
+        }
-            jones
+        out.println("</error>");
+      }
       //e.printStackTrace(out);
       out.println("</error>");
             jones
             jones
             jones
   /**
-            bojilova
+   * Parse XML Document to look for <!DOCTYPE ... PUBLIC/SYSTEM ... >
    * in order to decide whether to use validation parser
    */
   private static boolean validateXML(String xmltext) throws IOException {
     StringReader xmlreader = new StringReader(xmltext);
     StringBuffer cbuff = new StringBuffer();
     java.util.Stack st = new java.util.Stack();
     boolean validate = false;
     int c;
     int inx;
     // read from the stream until find the keywords
     while ( (st.empty() || st.size()<4) && ((c = xmlreader.read()) != -1) ) {
       cbuff.append((char)c);
       // "<!DOCTYPE" keyword is found; put it in the stack
       if ( (inx = cbuff.toString().indexOf("<!DOCTYPE")) != -1 ) {
         cbuff = new StringBuffer();
         st.push("<!DOCTYPE");
+      }
       // "PUBLIC" keyword is found; put it in the stack
       if ( (inx = cbuff.toString().indexOf("PUBLIC")) != -1 ) {
         cbuff = new StringBuffer();
         st.push("PUBLIC");
+      }
       // "SYSTEM" keyword is found; put it in the stack
       if ( (inx = cbuff.toString().indexOf("SYSTEM")) != -1 ) {
         cbuff = new StringBuffer();
         st.push("SYSTEM");
+      }
       // ">" character is found; put it in the stack
       // ">" is found twice: fisrt from <?xml ...?>
       // and second from <!DOCTYPE ... >
       if ( (inx = cbuff.toString().indexOf(">")) != -1 ) {
         cbuff = new StringBuffer();
         st.push(">");
+      }
+    }
     // close the stream
     xmlreader.close();
     // check the stack whether it contains the keywords:
     // "<!DOCTYPE", "PUBLIC" or "SYSTEM", and ">" in this order
     if ( st.size() == 4 ) {
       if ( ((String)st.pop()).equals(">") &&
            ( ((String)st.peek()).equals("PUBLIC") |
              ((String)st.pop()).equals("SYSTEM") ) &&
            ((String)st.pop()).equals("<!DOCTYPE") )  {
         validate = true;
+      }
+    }
 System.out.println("Validation is " + validate);
     return validate;
+  }
-            bojilova
+  // END OF INSERT/UPDATE SECTION
             bojilova
-            bojilova
+  // DELETE SECTION
-            bojilova
+  /**
-            jones
+   * Handle the database delete request and delete an XML document
    * from the database connection
    */
   private void handleDeleteAction(PrintWriter out, Hashtable params,
-            bojilova
+               HttpServletResponse response, String user, String[] groups) {
             jones
     String[] docid = (String[])params.get("docid");
             tao
-            jones
+    // delete the document from the database
     try {
             tao
-            jones
+                                      // NOTE -- NEED TO TEST HERE
-            jones
+                                      // FOR EXISTENCE OF DOCID PARAM
-            jones
+                                      // BEFORE ACCESSING ARRAY
-            berkley
+      try {
-            tao
+        DocumentImpl.delete(docid[0], user, groups);
-            jones
+        response.setContentType("text/xml");
         out.println("<?xml version=\"1.0\"?>");
         out.println("<success>");
-            jones
+        out.println("Document deleted.");
-            jones
+        out.println("</success>");
-            jones
+      } catch (AccessionNumberException ane) {
-            jones
+        response.setContentType("text/xml");
         out.println("<?xml version=\"1.0\"?>");
         out.println("<error>");
         out.println("Error deleting document!!!");
-            jones
+        out.println(ane.getMessage());
-            jones
+        out.println("</error>");
             jones
-            jones
+    } catch (Exception e) {
       response.setContentType("text/xml");
       out.println("<?xml version=\"1.0\"?>");
       out.println("<error>");
       out.println(e.getMessage());
       out.println("</error>");
             tao
             jones
-            bojilova
+  // END OF DELETE SECTION
             higgins
-            bojilova
+  // VALIDATE SECTION
-            higgins
+  /**
-            jones
+   * Handle the validation request and return the results to the requestor
-            higgins
+   */
-            jones
+  private void handleValidateAction(PrintWriter out, Hashtable params,
                HttpServletResponse response) {
             higgins
-            jones
+    // Get the document indicated
     String valtext = null;
-            tao
+    DBConnection dbConn = null;
     int serialNumber = -1;
             bojilova
-            jones
+    try {
       valtext = ((String[])params.get("valtext"))[0];
     } catch (Exception nullpe) {
             higgins
             tao
-            bojilova
+      String docid = null;
-            jones
+      try {
         // Find the document id number
-            jones
+        docid = ((String[])params.get("docid"))[0];
             bojilova
             tao
-            bojilova
+        // Get the document indicated from the db
-            tao
+        DocumentImpl xmldoc = new DocumentImpl(docid);
-            jones
+        valtext = xmldoc.toString();
             jones
-            jones
+      } catch (NullPointerException npe) {
-            jones
+        response.setContentType("text/xml");
         out.println("<error>Error getting document ID: " + docid + "</error>");
-            tao
+        //if ( conn != null ) { util.returnConnection(conn); }
-            jones
+        return;
-            bojilova
+      } catch (Exception e) {
         response.setContentType("text/html");
         out.println(e.getMessage());
             tao
             jones
             higgins
             tao
-            jones
+    try {
-            bojilova
+      // get a connection from the pool
-            tao
+      dbConn=DBConnectionPool.
                   getDBConnection("MetaCatServlet.handleValidateAction");
       serialNumber=dbConn.getCheckOutSerialNumber();
       DBValidate valobj = new DBValidate(saxparser,dbConn);
-            jones
+      boolean valid = valobj.validateString(valtext);
             higgins
       // set content type and other response header fields first
-            jones
+      response.setContentType("text/xml");
       out.println(valobj.returnErrors());
-            jones
+    } catch (NullPointerException npe2) {
       // set content type and other response header fields first
-            jones
+      response.setContentType("text/xml");
       out.println("<error>Error validating document.</error>");
-            bojilova
+    } catch (Exception e) {
       response.setContentType("text/html");
       out.println(e.getMessage());
     } finally {
-            tao
+      // Return db connection
       DBConnectionPool.returnDBConnection(dbConn, serialNumber);
             bojilova
             jones
-            bojilova
+  // END OF VALIDATE SECTION
   // OTHER ACTION HANDLERS
             bojilova
-            tao
+  /**
    * Handle "getrevsionanddoctype" action
    * Given a docid, return it's current revision and doctype from data base
    * The output is String look like "rev;doctype"
    */
   private void handleGetRevisionAndDocTypeAction(PrintWriter out,
                                                               Hashtable params)
+  {
     // To store doc parameter
     String [] docs = new String[10];
     // Store a single doc id
     String givenDocId = null;
     // Get docid from parameters
     if (params.containsKey("docid"))
+    {
       docs = (String[])params.get("docid");
+    }
     // Get first docid form string array
     givenDocId = docs[0];
     try
+    {
       // Make sure there is a docid
       if (givenDocId == null || givenDocId.equals(""))
+      {
         throw new Exception("User didn't specify docid!");
       }//if
       // Create a DBUtil object
       DBUtil dbutil = new DBUtil();
       // Get a rev and doctype
       String revAndDocType =
                 dbutil.getCurrentRevisionAndDocTypeForGivenDocument(givenDocId);
       out.println(revAndDocType);
     }//try
     catch (Exception e)
+    {
       // Handle exception
       out.println("<?xml version=\"1.0\"?>");
       out.println("<error>");
       out.println(e.getMessage());
       out.println("</error>");
     }//catch
   }//handleGetRevisionAndDocTypeAction
-            bojilova
+  /**
-            bojilova
+   * Handle "getaccesscontrol" action.
    * Read Access Control List from db connection in XML format
    */
   private void handleGetAccessControlAction(PrintWriter out, Hashtable params,
                                        HttpServletResponse response,
-            bojilova
+                                       String username, String[] groupnames) {
             bojilova
-            tao
+    DBConnection dbConn = null;
     int serialNumber = -1;
-            bojilova
+    String docid = ((String[])params.get("docid"))[0];
     try {
         // get connection from the pool
-            tao
+        dbConn=DBConnectionPool.
                  getDBConnection("MetaCatServlet.handleGetAccessControlAction");
         serialNumber=dbConn.getCheckOutSerialNumber();
         AccessControlList aclobj = new AccessControlList(dbConn);
-            bojilova
+        String acltext = aclobj.getACL(docid, username, groupnames);
-            bojilova
+        out.println(acltext);
     } catch (Exception e) {
       out.println("<?xml version=\"1.0\"?>");
       out.println("<error>");
       out.println(e.getMessage());
       out.println("</error>");
     } finally {
-            tao
+      // Retrun db connection to pool
       DBConnectionPool.returnDBConnection(dbConn, serialNumber);
             bojilova
+  }
   /**
-            bojilova
+   * Handle the "getprincipals" action.
    * Read all principals from authentication scheme in XML format
    */
   private void handleGetPrincipalsAction(PrintWriter out, String user,
                                          String password) {
             tao
-            bojilova
+    try {
             tao
-            bojilova
+        AuthSession auth = new AuthSession();
         String principals = auth.getPrincipals(user, password);
         out.println(principals);
     } catch (Exception e) {
       out.println("<?xml version=\"1.0\"?>");
       out.println("<error>");
       out.println(e.getMessage());
       out.println("</error>");
             tao
             bojilova
+  }
   /**
-            bojilova
+   * Handle "getdoctypes" action.
-            bojilova
+   * Read all doctypes from db connection in XML format
    */
   private void handleGetDoctypesAction(PrintWriter out, Hashtable params,
                                        HttpServletResponse response) {
             tao
-            bojilova
+    try {
             tao
         DBUtil dbutil = new DBUtil();
-            bojilova
+        String doctypes = dbutil.readDoctypes();
         out.println(doctypes);
     } catch (Exception e) {
       out.println("<?xml version=\"1.0\"?>");
       out.println("<error>");
       out.println(e.getMessage());
       out.println("</error>");
             tao
             bojilova
+  }
   /**
-            bojilova
+   * Handle the "getdtdschema" action.
    * Read DTD or Schema file for a given doctype from Metacat catalog system
    */
   private void handleGetDTDSchemaAction(PrintWriter out, Hashtable params,
                                         HttpServletResponse response) {
             tao
-            bojilova
+    String doctype = null;
     String[] doctypeArr = (String[])params.get("doctype");
     // get only the first doctype specified in the list of doctypes
     // it could be done for all doctypes in that list
     if (doctypeArr != null) {
         doctype = ((String[])params.get("doctype"))[0];
+    }
     try {
             tao
         DBUtil dbutil = new DBUtil();
-            bojilova
+        String dtdschema = dbutil.readDTDSchema(doctype);
         out.println(dtdschema);
     } catch (Exception e) {
       out.println("<?xml version=\"1.0\"?>");
       out.println("<error>");
       out.println(e.getMessage());
       out.println("</error>");
             tao
             bojilova
+  }
   /**
-            bojilova
+   * Handle the "getdataguide" action.
-            bojilova
+   * Read Data Guide for a given doctype from db connection in XML format
    */
   private void handleGetDataGuideAction(PrintWriter out, Hashtable params,
                                         HttpServletResponse response) {
             tao
-            bojilova
+    String doctype = null;
     String[] doctypeArr = (String[])params.get("doctype");
             bojilova
-            bojilova
+    // get only the first doctype specified in the list of doctypes
     // it could be done for all doctypes in that list
     if (doctypeArr != null) {
         doctype = ((String[])params.get("doctype"))[0];
+    }
-            bojilova
+    try {
             tao
         DBUtil dbutil = new DBUtil();
-            bojilova
+        String dataguide = dbutil.readDataGuide(doctype);
-            bojilova
+        out.println(dataguide);
     } catch (Exception e) {
       out.println("<?xml version=\"1.0\"?>");
       out.println("<error>");
       out.println(e.getMessage());
       out.println("</error>");
             tao
             bojilova
+  }
-            bojilova
+  /**
    * Handle the "getlastdocid" action.
    * Get the latest docid with rev number from db connection in XML format
    */
-            jones
+  private void handleGetMaxDocidAction(PrintWriter out, Hashtable params,
-            bojilova
+                                        HttpServletResponse response) {
             tao
-            jones
+    String scope = ((String[])params.get("scope"))[0];
     if (scope == null) {
         scope = ((String[])params.get("username"))[0];
+    }
             bojilova
     try {
             tao
         DBUtil dbutil = new DBUtil();
-            jones
+        String lastDocid = dbutil.getMaxDocid(scope);
-            bojilova
+        out.println("<?xml version=\"1.0\"?>");
         out.println("<lastDocid>");
-            jones
+        out.println("  <scope>" + scope + "</scope>");
-            bojilova
+        out.println("  <docid>" + lastDocid + "</docid>");
         out.println("</lastDocid>");
     } catch (Exception e) {
       out.println("<?xml version=\"1.0\"?>");
       out.println("<error>");
       out.println(e.getMessage());
       out.println("</error>");
             tao
             bojilova
+  }
-            jones
+  /**
    * Handle documents passed to metacat that are encoded using the
    * "multipart/form-data" mime type.  This is typically used for uploading
    * data files which may be binary and large.
    */
   private void handleMultipartForm(HttpServletRequest request,
                                    HttpServletResponse response)
+  {
     PrintWriter out = null;
     String action = null;
     // Parse the multipart form, and save the parameters in a Hashtable and
     // save the FileParts in a hashtable
     Hashtable params = new Hashtable();
     Hashtable fileList = new Hashtable();
     try {
       // MBJ: need to put filesize limit in Metacat config (metacat.properties)
-            tao
+      MultipartParser mp = new MultipartParser(request, 200*1024*1024); //200MB
-            jones
+      Part part;
       while ((part = mp.readNextPart()) != null) {
         String name = part.getName();
         if (part.isParam()) {
           // it's a parameter part
           ParamPart paramPart = (ParamPart) part;
           String value = paramPart.getStringValue();
           params.put(name, value);
           if (name.equals("action")) {
             action = value;
+          }
         } else if (part.isFile()) {
           // it's a file part
           FilePart filePart = (FilePart) part;
           fileList.put(name, filePart);
           // Stop once the first file part is found, otherwise going onto the
           // next part prevents access to the file contents.  So...for upload
           // to work, the datafile must be the last part
           break;
+        }
+      }
     } catch (IOException ioe) {
       try {
         out = response.getWriter();
       } catch (IOException ioe2) {
         System.err.println("Fatal Error: couldn't get response output stream.");
+      }
       out.println("<?xml version=\"1.0\"?>");
       out.println("<error>");
       out.println("Error: problem reading multipart data.");
       out.println("</error>");
+    }
     // Get the session information
     String username = null;
     String password = null;
-            bojilova
+    String[] groupnames = null;
-            jones
+    String sess_id = null;
     // be aware of session expiration on every request
     HttpSession sess = request.getSession(true);
     if (sess.isNew()) {
       // session expired or has not been stored b/w user requests
       username = "public";
       sess.setAttribute("username", username);
     } else {
       username = (String)sess.getAttribute("username");
       password = (String)sess.getAttribute("password");
-            bojilova
+      groupnames = (String[])sess.getAttribute("groupnames");
-            jones
+      try {
         sess_id = (String)sess.getId();
       } catch(IllegalStateException ise) {
         System.out.println("error in  handleMultipartForm: this shouldn't " +
                            "happen: the session should be valid: " +
                            ise.getMessage());
+      }
+    }
             tao
     // Get the out stream
     try {
-            jones
+          out = response.getWriter();
         } catch (IOException ioe2) {
-            tao
+          util.debugMessage("Fatal Error: couldn't get response "+
                                                               "output stream.");
             jones
             tao
     if ( action.equals("upload")) {
       if (username != null &&  !username.equals("public")) {
         handleUploadAction(request, out, params, fileList,
                            username, groupnames);
       } else {
-            jones
+        out.println("<?xml version=\"1.0\"?>");
         out.println("<error>");
         out.println("Permission denied for " + action);
         out.println("</error>");
+      }
     } else {
-            tao
+      /*try {
-            jones
+        out = response.getWriter();
       } catch (IOException ioe2) {
         System.err.println("Fatal Error: couldn't get response output stream.");
-            tao
+      }*/
-            jones
+      out.println("<?xml version=\"1.0\"?>");
       out.println("<error>");
       out.println("Error: action not registered.  Please report this error.");
       out.println("</error>");
+    }
-            tao
+    out.close();
             jones
   /**
    * Handle the upload action by saving the attached file to disk and
    * registering it in the Metacat db
    */
   private void handleUploadAction(HttpServletRequest request,
-            tao
+                                  PrintWriter out,
-            jones
+                                  Hashtable params, Hashtable fileList,
-            bojilova
+                                  String username, String[] groupnames)
             jones
-            tao
+    //PrintWriter out = null;
-            tao
+    //Connection conn = null;
-            jones
+    String action = null;
     String docid = null;
             tao
-            tao
+    /*response.setContentType("text/xml");
-            tao
+    try
+    {
-            jones
+      out = response.getWriter();
             tao
     catch (IOException ioe2)
+    {
-            jones
+      System.err.println("Fatal Error: couldn't get response output stream.");
-            tao
+    }*/
             jones
-            tao
+    if (params.containsKey("docid"))
+    {
-            jones
+      docid = (String)params.get("docid");
+    }
     // Make sure we have a docid and datafile
     if (docid != null && fileList.containsKey("datafile")) {
       // Get a reference to the file part of the form
       FilePart filePart = (FilePart)fileList.get("datafile");
       String fileName = filePart.getFileName();
-            tao
+      MetaCatUtil.debugMessage("Uploading filename: " + fileName, 10);
             jones
       // Check if the right file existed in the uploaded data
       if (fileName != null) {
-            tao
+        try
+        {
-            tao
+           //MetaCatUtil.debugMessage("Upload datafile " + docid +"...", 10);
-            tao
+           //If document get lock data file grant
-            tao
+           if (DocumentImpl.getDataFileLockGrant(docid))
+           {
-            tao
+              // register the file in the database (which generates an exception
-            tao
+              //if the docid is not acceptable or other untoward things happen
               DocumentImpl.registerDocument(fileName, "BIN", docid, username);
             jones
-            tao
+              // Save the data file to disk using "docid" as the name
               dataDirectory.mkdirs();
               File newFile = new File(dataDirectory, docid);
               long size = filePart.writeTo(newFile);
             tao
               // Force replication this data file
               // To data file, "insert" and update is same
               // The fourth parameter is null. Because it is notification server
               // and this method is in MetaCatServerlet. It is original command,
               // not get force replication info from another metacat
               ForceReplicationHandler frh = new ForceReplicationHandler
                                                 (docid, "insert", false, null);
-            tao
+              // set content type and other response header fields first
               out.println("<?xml version=\"1.0\"?>");
               out.println("<success>");
               out.println("<docid>" + docid + "</docid>");
               out.println("<size>" + size + "</size>");
               out.println("</success>");
-            tao
+          }//if
             jones
-            tao
+        } //try
-            tao
+        catch (Exception e)
+        {
-            jones
+          out.println("<?xml version=\"1.0\"?>");
           out.println("<error>");
           out.println(e.getMessage());
           out.println("</error>");
+        }
             tao
             tao
       else
+      {
-            jones
+        // the field did not contain a file
         out.println("<?xml version=\"1.0\"?>");
         out.println("<error>");
         out.println("The uploaded data did not contain a valid file.");
         out.println("</error>");
+      }
             tao
     else
+    {
-            jones
+      // Error bcse docid missing or file missing
       out.println("<?xml version=\"1.0\"?>");
       out.println("<error>");
       out.println("The uploaded data did not contain a valid docid " +
                   "or valid file.");
       out.println("</error>");
+    }
+  }
             jones

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