Metacat

            sql.append(docid).append("'");

        }

        pstmt = dbconn.prepareStatement(sql.toString());

        pstmt.execute();

        pstmt.close();

//        String doc = docid;

      double afterPutNode = System.currentTimeMillis()/1000;

      double afterDelete = 0;

        // Opening separate db connection for deleting and writing

        // XML Index -- be sure that it is all in one db transaction

                // Lastly, update the xml_path_index table

                if(!pathsFound.isEmpty()){

                    try {

                    	updatePathIndex(dbConn, pathsFound);

                    } catch (SQLException sqle) {

								+ docid);

			}

		} catch (PropertyNotFoundException pnfe) {

					+ "cache not run for docid: " + docid + " : " + pnfe.getMessage());

		} catch (StringIndexOutOfBoundsException siobe) {

			logMetacat.error("DocumentImpl.buildIndex -  String indexing problem.  Spatial " 

                if (current.getNodeType().equals("ATTRIBUTE")) {

                    currentName = "@" + currentName;

                }

                if ( currentName != null ) {

                  if ( !currentName.equals("") ) {

                    pathList.put(currentName, new PathIndexEntry(leafNodeId,

                }

				if (pathsForIndexing.contains(currentName)

						&& leafData.trim().length() != 0) {

					pathsFoundForIndexing.put(currentName, new PathIndexEntry(

							leafNodeId, currentName, docid, leafParentId, leafData,

							leafDataNumerical));

            String path = current.getNodeName() + children;

            if ( !children.equals("") ) {

                pathList.put(path, new PathIndexEntry(leafNodeId, path, docid,

                    doctype, parentId));

				if (pathsForIndexing.contains(path)

						&& leafData.trim().length() != 0) {

					pathsFoundForIndexing.put(path, new PathIndexEntry(leafNodeId,

							path, docid, leafParentId, leafData, leafDataNumerical));

				}

                if ( !path.equals("") ) {

                  fullPath = '/' + path;

                }

                pathList.put(fullPath, new PathIndexEntry(leafNodeId, fullPath,

                    docid, doctype, parentId));

				if (pathsForIndexing.contains(fullPath)

						&& leafData.trim().length() != 0) {

					pathsFoundForIndexing.put(fullPath, new PathIndexEntry(

							leafNodeId, fullPath, docid, leafParentId, leafData,

							leafDataNumerical));

    	double start = System.currentTimeMillis()/1000;

        String familyId = docid;

        String sql = "DELETE FROM xml_index WHERE docid = ?";

        PreparedStatement pstmt = conn.prepareStatement(sql);

        // Execute the delete and close the statement

        pstmt.setString(1, familyId);

        int rows = pstmt.executeUpdate();

        pstmt.close();

        logMetacat.debug("DocumentImpl.deleteNodeIndex - Deleted " + rows + " rows from xml_index " +

        pstmt = conn.prepareStatement(

                "DELETE FROM xml_path_index WHERE docid = ?");

        pstmt.setString(1, docid);

        rows = pstmt.executeUpdate();

        conn.increaseUsageCount(1);

        pstmt.close();

        Iterator<PathIndexEntry> it = pathList.values().iterator();

        while (it.hasNext()) {

        	 PathIndexEntry entry = (PathIndexEntry)it.next();

        	 pstmt.setLong(1, entry.nodeId);

        	 pstmt.setString(2, entry.path);

        	 pstmt.setLong(5, entry.parentId);

        	 pstmt.executeUpdate();

         }

        // Close the database statement

             pstmt.setString(2, entry.path);

             pstmt.setString(3, entry.nodeData);

             pstmt.setFloat(4, entry.nodeDataNumerical);

             pstmt.execute();

        }

        // Close the database statement

            serialNumber = dbconn.getCheckOutSerialNumber();

            pstmt = dbconn.prepareStatement("select rev from xml_documents "

                    + "where docid like '" + newid + "'");

            pstmt.execute();

            ResultSet rs = pstmt.getResultSet();

            boolean tablehasrows = rs.next();

            pstmt = dbconn.prepareStatement(sql.toString());

            pstmt.execute();

            ResultSet rs = pstmt.getResultSet();

            boolean tableHasRows = rs.next();

            //because connection use twice here, so we need to increase one

            dbconn.increaseUsageCount(1);

            pstmt.setInt(1, serverlocation);

            pstmt.execute();

            rs = pstmt.getResultSet();

            tableHasRows = rs.next();

                // Bind the values to the query

                pstmt.setString(1, doctype);

                pstmt.execute();

                rs = pstmt.getResultSet();

                tableHasRows = rs.next();

            // Bind the values to the query

            pstmt.setLong(1, rootnodeid);

            //System.out.println("in getNodeREcorelist !!!!!!!!!!!4");

            pstmt.execute();

            ResultSet rs = pstmt.getResultSet();

            //System.out.println("in getNodeREcorelist !!!!!!!!!!!5");

            } else if (action.equals("UPDATE")) {

                int thisrev = DBUtil.getLatestRevisionInDocumentTable(docid);

                // Save the old document publicaccessentry in a backup table

                thisdoc = new DocumentImpl(accNumber, false);

                DocumentImpl.archiveDocAndNodesRevision(connection, docid, user, thisdoc);

                //if the updated vesion is not greater than current one,

                //throw it into a exception

                if (rev <= thisrev) {

                    //set the user specified revision

                    thisrev = rev;

                }

                boolean useXMLIndex = (new Boolean(PropertyService

                        .getProperty("database.usexmlindex"))).booleanValue();

                if (useXMLIndex) {

                    double start = System.currentTimeMillis()/1000;

                    // Delete index for the old version of docid

                    // The new index is inserting on the next calls to DBSAXNode

                    pstmt = connection

                            .prepareStatement("DELETE FROM xml_index WHERE docid='"

                                    + this.docid + "'");

                    // Increase dbconnection usage count

                    connection.increaseUsageCount(1);

                    pstmt.execute();

                    pstmt.close();

                    double end = System.currentTimeMillis()/1000;

                }

                // Update the new document to reflect the new node tree

                }

            } else {

            }

            // Do the insertion

            pstmt.execute();

            pstmt.close();

                pstmt.setLong(1, thisdoc.getRootNodeID());

                pstmt.execute();

                pstmt.close();*/

            }

        } catch (SQLException sqle) {

            sqle.printStackTrace();

            throw sqle;

        } catch (Exception e) {

            e.printStackTrace();

            throw e;

        }

            //bind variable

            pstate.setString(1, docid);

            //excute query

            pstate.execute();

            //handle resultset

            rs = pstate.getResultSet();

            pstmt = conn.prepareStatement("SELECT * FROM xml_documents "

                                          + "WHERE docid = ?");

            pstmt.setString(1, docid);

            pstmt.execute();

            ResultSet rs = pstmt.getResultSet();

            if(!rs.next()){

            pstmt = conn

                    .prepareStatement("DELETE FROM xml_index WHERE docid = ?");

            pstmt.setString(1, docid);

            pstmt.execute();

            pstmt.close();

            conn.increaseUsageCount(1);

            pstmt = conn.prepareStatement(

                    "DELETE FROM xml_access WHERE accessfileid = ?");

            pstmt.setString(1, docid);

            pstmt.execute();

            pstmt.close();

            conn.increaseUsageCount(1);

            pstmt = conn.prepareStatement(

                    "DELETE FROM xml_access WHERE docid = ?");

            pstmt.setString(1, docid);

            pstmt.execute();

            pstmt.close();

            conn.increaseUsageCount(1);

         	   DBQuery.clearQueryResultCache();

            }

           double end = System.currentTimeMillis()/1000;

        } catch (Exception e) {

            logMetacat.error("DocumentImpl.delete - General error: " + e.getMessage());

        pstmt.setString(1, docid);

        pstmt.setString(2, user);

        pstmt.setString(3, docid);

        pstmt.execute();

        pstmt.close();

        double end = System.currentTimeMillis()/1000;

        dbconn.increaseUsageCount(1);

        // Bind the values to the query and execute it

        pstmt.setLong(1, rootNodeId);

        pstmt.execute();

        pstmt.close();

        double end = System.currentTimeMillis()/1000;

            pstmt.setString(1, docid);

            pstmt.setString(2, user);

            pstmt.setString(3, docid);

            pstmt.execute();

            pstmt.close();

        } catch (SQLException e) {

            //delete a record

            pStmt = conn.prepareStatement(

                    "DELETE FROM xml_documents WHERE docid = '" + docId + "'");

            pStmt.execute();

        } finally {

            try {

                                + ", '" + replicate + "', '" + dataReplicate

                                + "','" + hub + "')");

                pStmt.execute();

                dbConn.commit();

                // Increase usage number

              }

            }

            // Do the insertion

            pstmt.execute();

            pstmt.close();

            logMetacat.debug("DocumentImpl.writeDocumentToRevisionTable - end of write into revisons");

        } 

        catch (SQLException sqle) 

        {

        	sqle.printStackTrace();

            throw sqle;

        } 

        catch (Exception e) 

        {

            e.printStackTrace();

            throw e;

        }

    static private void deleteXMLNodes(DBConnection dbconn, long rootId) throws Exception

    {

//        AccessionNumber ac;

        PreparedStatement pstmt = null;

        double start = System.currentTimeMillis()/1000;

        String sql = "DELETE FROM xml_nodes WHERE rootnodeid ="+ rootId;

        pstmt = dbconn.prepareStatement(sql);

        // Increase dbconnection usage count

        dbconn.increaseUsageCount(1);

        pstmt.execute();

        pstmt.close(); 

        double end = System.currentTimeMillis()/1000;