Metacat

package edu.ucsb.nceas.metacat;

import java.sql.PreparedStatement;

import org.apache.log4j.Logger;

import edu.ucsb.nceas.metacat.database.DBConnection;

import edu.ucsb.nceas.metacat.database.DBConnectionPool;

import edu.ucsb.nceas.metacat.properties.PropertyService;

/**

 * Before Metacat 1.8.1 release, Metacat uses the eml201 schema with the tag

 * RELEASE_EML_2_0_1_UPDATE_5. Unfortunately, this tag points at wrong version

 * of eml-resource.xsd. In this schema, the element "references" has an attribute named

 * "system" and the attribute has a default value "document". Metacat will add 

 * the attribute system="document" to "references" element even the orginal eml didn't have it

 * (this is another bug and see bug 1601), so this causes metacat generated some invalid eml201

 * documents. This class provides a path to fix the existed invalid eml201 documents. It will

 * remove the attribute system="document" of the element "references" in xml_nodes and xml_index

 * tables. 

 * @author tao

 *

 */

public class EML201DocumentCorrector  

{

	private Logger logMetacat = Logger.getLogger(EML201DocumentCorrector.class);

	/**

	 * Default constructor

	 *

	 */

     public EML201DocumentCorrector()

     {

     }

     /**

      *  It will remove the records - attribute system="document" of element "refrence"

      *  in both xml_nodes and xml_index table. Since xml_index has a foreign key (nodeid)which

      *  references nodeid in xml_nodes table, we should delete records in xml_index table first.

      */

     public boolean run()

     {

    	 DBConnection dbconn = null;

    	 boolean success = false;

    	 int serialNumber = 0;

    	   try

    	      {

    	           //checkout the dbconnection

    	          dbconn = DBConnectionPool.getDBConnection("EML201DocumentCorrector.run");

    	          serialNumber = dbconn.getCheckOutSerialNumber();

    	          PreparedStatement deletingStatement = null;

    	          // delete the records in xml_index table 

    	          String deletingIndex = generateXML_IndexDeletingSQL();

    	          logMetacat.debug("EML201DocumentCorrector.run - deleting the records in xml_index table with sql: " + deletingIndex);

    	          deletingStatement = dbconn.prepareStatement(deletingIndex);

    	          deletingStatement.execute();

    	          deletingStatement.close();

    	          // delete the records in xml_nodes table

    	          String deletingNode = generateXML_NodeDeletingSQL();

    	          logMetacat.debug("EML201DocumentCorrector.run - deleting the records in xml_nodes table with sql: " + deletingNode);

    	          deletingStatement = dbconn.prepareStatement(deletingNode);

    	          deletingStatement.execute();

    	          deletingStatement.close();

    	          // delete the records in xml_nodes_revisions table

    	          String deletingNodeRevision = generateXML_Node_RevisionsDeletingSQL();

    	          logMetacat.debug("EML201DocumentCorrector.run - deleting the records in xml_nodes_revisions table with sql: " + deletingNodeRevision);

    	          deletingStatement = dbconn.prepareStatement(deletingNodeRevision);

    	          deletingStatement.execute();

    	          deletingStatement.close();

    	          success = true;

    	      }

    	        catch (Exception ee)

    	        {

    	          logMetacat.error("EML201DocumentCorrector.run: "

    	                                   + ee.getMessage());

    	          ee.printStackTrace();

    	        }

    	        finally

    	        {

    	          DBConnectionPool.returnDBConnection(dbconn, serialNumber);

    	        } //finally

    	        return success;

     }

     /*

      * Generate the sql command to delete the records in xml_node table.

      * Since it is leaf node, so we can just delete it without any other side-effect.

      */

     private String generateXML_NodeDeletingSQL()

     {

    	 String sql ="delete from xml_nodes where nodetype='ATTRIBUTE' and nodename='system' "+

    	                     "and parentnodeid in (select nodeid from xml_nodes where  nodetype='ELEMENT' and nodename='references') and docid in "+

    	                     "(select docid from xml_documents where doctype ='eml://ecoinformatics.org/eml-2.0.1')";

    	 return sql;

     }

     /*

      * Generate the sql command to delete the records in xml_node table.

      * Since it is leaf node, so we can just delete it without any other side-effect.

      */

     private String generateXML_Node_RevisionsDeletingSQL()

     {

    	 String sql ="delete from xml_nodes_revisions where nodetype='ATTRIBUTE' and nodename='system' "+

    	                     "and parentnodeid in (select nodeid from xml_nodes_revisions where  nodetype='ELEMENT' and nodename='references') and docid in "+

    	                     "(select docid from xml_revisions where doctype ='eml://ecoinformatics.org/eml-2.0.1')";

    	 return sql;

     }

     /*

      * Generate the sql command to delete the records in xml_nidex table;

      */

     private String generateXML_IndexDeletingSQL()

     {

    	 String sql ="delete from xml_index where doctype ='eml://ecoinformatics.org/eml-2.0.1' AND nodeid in "+ 

    	 "(select nodeid from xml_index where path ='references/@system')";

    	 return sql;

     }

     /**

      *  Runs the job to correct eml201 documents - deleting extral nodes in

      * @param argus

      * @throws Exception

      */

     public static void main(String[] args) throws Exception

     {

    	 //initialize options and connection pool

    	 PropertyService.getInstance(args[0]);

    	 DBConnectionPool connPool = DBConnectionPool.getInstance();

    	 // run the thread

    	 EML201DocumentCorrector correct = new EML201DocumentCorrector();

    	 //Thread thread = new Thread(correct);

    	 //thread.start();

    	 correct.run();

     }

}