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package edu.ucsb.nceas.metacat;
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import java.io.File;
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import java.sql.Statement;
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import org.apache.log4j.Logger;
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import edu.ucsb.nceas.utilities.Options;
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/**
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* Before Metacat 1.8.1 release, Metacat uses the eml201 schema with the tag
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* RELEASE_EML_2_0_1_UPDATE_5. Unfortunately, this tag points at wrong version
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* of eml-resource.xsd. In this schema, the element "references" has an attribute named
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* "system" and the attribute has a default value "document". Metacat will add
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* the attribute system="document" to "references" element even the orginal eml didn't have it
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* (this is another bug and see bug 1601), so this causes metacat generated some invalid eml201
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* documents. This class provides a path to fix the existed invalid eml201 documents. It will
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* remove the attribute system="document" of the element "references" in xml_nodes and xml_index
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* tables.
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* @author tao
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*
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*/
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public class EML201DocumentCorrector
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{
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private Logger logMetacat = Logger.getLogger(EML201DocumentCorrector.class);
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/**
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* Default constructor
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*
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*/
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public EML201DocumentCorrector()
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{
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}
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/**
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* It will remove the records - attribute system="document" of element "refrence"
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* in both xml_nodes and xml_index table. Since xml_index has a foreign key (nodeid)which
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* references nodeid in xml_nodes table, we should delete records in xml_index table first.
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*/
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public void run()
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{
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DBConnection dbconn = null;
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int serialNumber = 0;
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try
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{
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//checkout the dbconnection
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dbconn = DBConnectionPool.getDBConnection("DBQuery.findDocuments");
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serialNumber = dbconn.getCheckOutSerialNumber();
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Statement deletingStatement = dbconn.createStatement();
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// delete the records in xml_index table
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String deletingIndex = generateXML_IndexDeletingSQL();
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deletingStatement.execute(deletingIndex);
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// delete the records in xml_nodes table
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String deletingNode = generateXML_NodeDeletingSQL();
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deletingStatement.execute(deletingNode);
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// delete the records in xml_nodes_revisions table
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String deletingNodeRevision = generateXML_Node_RevisionsDeletingSQL();
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deletingStatement.execute(deletingNodeRevision);
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//close statement and connection
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deletingStatement.close();
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dbconn.close();
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}
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catch (Exception ee)
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{
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logMetacat.error("Exception in DBQuery.findDocuments: "
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+ ee.getMessage());
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ee.printStackTrace();
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}
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finally
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{
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DBConnectionPool.returnDBConnection(dbconn, serialNumber);
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} //finally
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}
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/*
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* Generate the sql command to delete the records in xml_node table.
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* Since it is leaf node, so we can just delete it without any other side-effect.
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*/
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private String generateXML_NodeDeletingSQL()
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{
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String sql ="delete from xml_nodes where nodetype='ATTRIBUTE' and nodename='system' and nodedata='document' "+
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"and parentnodeid in (select nodeid from xml_nodes where nodetype='ELEMENT' and nodename='references') and docid in "+
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"(select docid from xml_documents where doctype ='eml://ecoinformatics.org/eml-2.0.1')";
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return sql;
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}
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/*
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* Generate the sql command to delete the records in xml_node table.
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* Since it is leaf node, so we can just delete it without any other side-effect.
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*/
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private String generateXML_Node_RevisionsDeletingSQL()
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{
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String sql ="delete from xml_nodes_revisions where nodetype='ATTRIBUTE' and nodename='system' and nodedata='document' "+
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"and parentnodeid in (select nodeid from xml_nodes where nodetype='ELEMENT' and nodename='references') and docid in "+
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"(select docid from xml_documents where doctype ='eml://ecoinformatics.org/eml-2.0.1')";
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return sql;
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}
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/*
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* Generate the sql command to delete the records in xml_nidex table;
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*/
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private String generateXML_IndexDeletingSQL()
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{
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String sql ="delete from xml_index where doctype ='eml://ecoinformatics.org/eml-2.0.1' AND nodeid in "+
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"(select nodeid from xml_index where path ='references/@system')";
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return sql;
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}
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/**
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* Runs the job to correct eml201 documents - deleting extral nodes in
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* @param argus
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* @throws Exception
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*/
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public static void main(String[] argus) throws Exception
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{
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//initialize options and connection pool
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Options.initialize(new File("build/metacat.properties"));
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DBConnectionPool connPool = DBConnectionPool.getInstance();
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// run the thread
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EML201DocumentCorrector correct = new EML201DocumentCorrector();
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//Thread thread = new Thread(correct);
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//thread.start();
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correct.run();
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}
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}
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