Metacat

/**

 *  '$RCSfile$'

 *    Purpose: A Class that represents an XML document

 *  Copyright: 2000 Regents of the University of California and the

 *             National Center for Ecological Analysis and Synthesis

 *    Authors: Matt Jones

 *    Release: @release@

 *

 *   '$Author$'

 *     '$Date$'

 * '$Revision$'

 * 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

package edu.ucsb.nceas.metacat;

import java.sql.*;

import java.io.FileReader;

import java.io.IOException;

import java.io.StringWriter;

import java.io.Writer;

import java.util.Date;

import org.xml.sax.AttributeList;

import org.xml.sax.ContentHandler;

import org.xml.sax.DTDHandler;

import org.xml.sax.EntityResolver;

import org.xml.sax.ErrorHandler;

import org.xml.sax.InputSource;

import org.xml.sax.XMLReader;

import org.xml.sax.SAXException;

import org.xml.sax.SAXParseException;

import org.xml.sax.helpers.XMLReaderFactory;

 * A class that represents an XML document. It can be created with a simple

 * XML text document to a database connection using SAX.

public class DocumentImpl {

   public static final String DTD                    = "DTD";

              "http://apache.org/xml/properties/schema/external-schemaLocation";

                            "http://xml.org/sax/properties/declaration-handler";

   public static final String LEXICALPROPERTY =

                             "http://xml.org/sax/properties/lexical-handler";

   public static final String VALIDATIONFEATURE =

                             "http://xml.org/sax/features/validation";

   public static final String SCHEMAVALIDATIONFEATURE =

                             "http://apache.org/xml/features/validation/schema";

   public static final String NAMESPACEFEATURE =

                              "http://xml.org/sax/features/namespaces";

   public static final String NAMESPACEPREFIXESFEATURE =

                              "http://xml.org/sax/features/namespace-prefixes";

                                         // "eml://ecoinformatics.org/eml-2.0.0";

  static final int WRITE = 2;

  static final int READ = 4;

  private String doctype = null;

//  private String doctitle = null;

  private String updatedate = null;

  private String userupdated = null;

  private ElementNode rootNode = null;

  //ReplicationServerList serverList = new ReplicationServerList();

  /**

   * from the database.  If readNodes is false, then the node data is not

   * read at this time, but is deferred until it is needed (such as when a

   * call to toXml() is made).

   * @param conn the database connection from which to read the document

   * @param readNodes flag indicating whether the xmlnodes should be read

      // Look up the document information

      getDocumentInfo(docid);

        // The sort order of the records is determined by the NodeComparator

        // class, and needs to represent a depth-first traversal for the

        // toXml() method to work properly

        nodeRecordList = getNodeRecordList(rootnodeid);

      throw ex;

    } catch (Throwable t) {

      throw new McdbException("Error reading document from " +

                              "DocumentImpl.DocumentImpl: " + docid);

  /**

   * for reading the document

   * @param conn the database connection from which to read the document

   * @param docid the identifier of the document to be created

   */

   * Construct a new document instance, writing the contents to the database.

   * This method is called from DBSAXHandler because we need to know the

   * root element name for documents without a DOCTYPE before creating it.

   *

   * In this constructor, the docid is without rev. There is a string rev to

   * specify the revision user want to upadate. The revion is only need to be

   * greater than current one. It is not need to be sequent number just after

   * current one. So it is only used in update action

   * @param conn the JDBC Connection to which all information is written

   * @param rootnodeid - sequence id of the root node in the document

   * @param docname - the name of DTD, i.e. the name immediately following

   *        the DOCTYPE keyword ( should be the root element name ) or

   *        the root element name if no DOCTYPE declaration provided

   *        (Oracle's and IBM parsers are not aware if it is not the

   *        root element name)

   * @param doctype - Public ID of the DTD, i.e. the name immediately

   *                  following the PUBLIC keyword in DOCTYPE declaration or

   *                  the docname if no Public ID provided or

   *                  null if no DOCTYPE declaration provided

   * @param docid the docid to use for the UPDATE, no version number

   * @param version, need to be update

   * @param action the action to be performed (INSERT OR UPDATE)

   * @param user the user that owns the document

   * @param pub flag for public "read" access on document

   * @param serverCode the serverid from xml_replication on which this document

   *        resides.

   *

   */

                      String action, String user,

                      String pub, String catalogId, int serverCode)

                      throws SQLException, Exception

  {

    this.docname = docName;

    this.doctype = docType;

    this.docid = docId;

    this.updatedVersion = newRevision;

    writeDocumentToDB(action, user, pub, catalogId, serverCode);

  }

   */

  public static void registerDocument(

                     String docname, String doctype, String accnum, String user)

                     throws SQLException, AccessionNumberException, Exception

  {

    {

      int serverLocation=getServerLocationNumber(accnum);

    }

    catch (Exception e)

    {

      throw e;

    }

  }

  /**

   * (ie, just an entry in xml_documents, nothing in xml_nodes).

   * Creates a reference to a filesystem document (used for non-xml data files).

   * @param docname - the name of DTD, i.e. the name immediately following

   *        the DOCTYPE keyword ( should be the root element name ) or

   *        the root element name if no DOCTYPE declaration provided

   *        (Oracle's and IBM parsers are not aware if it is not the

   *        root element name)

   * @param doctype - Public ID of the DTD, i.e. the name immediately

   *                  following the PUBLIC keyword in DOCTYPE declaration or

   *                  the docname if no Public ID provided or

   *                  null if no DOCTYPE declaration provided

   * @param accnum the accession number to use for the INSERT OR UPDATE, which

   *               includes a revision number for this revision of the document

   *               (e.g., knb.1.1)

   * @param user the user that owns the document

   * @param serverCode the serverid from xml_replication on which this document

   *        resides.

   */

  public static void registerDocument(

                     String docname, String doctype, String accnum,

                     String user, int serverCode)

                     throws SQLException, AccessionNumberException, Exception

  {

    int serialNumber = -1;

    PreparedStatement pstmt = null;

    //MetaCatUtil util = new MetaCatUtil();

      //check out DBConnection

      dbconn=DBConnectionPool.

                    getDBConnection("DocumentImpl.registerDocument");

      serialNumber=dbconn.getCheckOutSerialNumber();

      int userSpecifyRev=MetaCatUtil.getVersionFromString(accnum);

      //the data file is a new one, inert it into table

      //user specified rev should be great than 0

      if (revInDataBase==-1 && userSpecifyRev>0 )

      {

      //rev is greater the last revsion number and revInDataBase isn't -1

      // it is a updated data file

      else if (userSpecifyRev>revInDataBase && revInDataBase>0)

      {

        //archive the old entry

      //other situation

      else

      {

        throw new Exception("Revision number couldn't be "

                    +userSpecifyRev);

      }

      String rev = ac.getRev();

      String dateString = formatter.format(localtime);

      String  sqlDateString = dbAdapter.getDateTimeFunction();

      StringBuffer sql = new StringBuffer();

      {

        sql.append("insert into xml_documents (docid, docname, doctype, ");

        sql.append("user_owner, user_updated, server_location, rev,date_created");

        sql.append(", date_updated, public_access) values ('");

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

        sql.append(docname).append("','");

        sql.append(doctype).append("','");

        sql.append(user).append("','");

        sql.append(user).append("','");

        sql.append(serverCode).append("','");

        sql.append(rev).append("',");

        sql.append(sqlDateString).append(",");

        sql.append(sqlDateString).append(",");

        sql.append("'0')");

      }

      else if (action != null && action.equals("update"))

      {

        sql.append("update xml_documents set docname ='");

        sql.append(docname).append("', ");

        sql.append("user_updated='");

        sql.append(user).append("', ");

        sql.append("server_location='");

        sql.append(serverCode).append("',");

        sql.append("rev='");

        sql.append(rev).append("',");

        sql.append("date_updated=");

        sql.append(sqlDateString);

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

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

      }

      pstmt.close();

    finally

    {

      try

      {

  }

   * Register a document that resides on the filesystem with the database.

   * (ie, just an entry in xml_documents, nothing in xml_nodes).

   * Creates a reference to a filesystem document (used for non-xml data files)

   * This method will be called for register data file in xml_documents in

   * Replication.

   * This method is revised from registerDocument.

   *

   * @param conn the JDBC Connection to which all information is written

   * @param docname - the name of DTD, i.e. the name immediately following

   *        the DOCTYPE keyword ( should be the root element name ) or

   *        the root element name if no DOCTYPE declaration provided

   *        (Oracle's and IBM parsers are not aware if it is not the

   *        root element name)

   * @param doctype - Public ID of the DTD, i.e. the name immediately

   *                  following the PUBLIC keyword in DOCTYPE declaration or

   *                  the docname if no Public ID provided or

   *                  null if no DOCTYPE declaration provided

   * @param accnum the accession number to use for the INSERT OR UPDATE, which

   *               includes a revision number for this revision of the document

   *               (e.g., knb.1.1)

   * @param user the user that owns the document

   * @param serverCode the serverid from xml_replication on which this document

   *        resides.

   */

  public static void registerDocumentInReplication(

                     String docname, String doctype, String accnum,

                     String user, int serverCode)

                     throws SQLException, AccessionNumberException, Exception

  {

    int serialNumber = -1;

    //MetaCatUtil util = new MetaCatUtil();

       dbconn=DBConnectionPool.

                  getDBConnection("DocumentImpl.registerDocumentInReplication");

      serialNumber=dbconn.getCheckOutSerialNumber();

      int userSpecifyRev=MetaCatUtil.getVersionFromString(accnum);

      //the data file is a new one, inert it into table

      //user specified rev should be great than 0

      if (revInDataBase==-1 && userSpecifyRev>0 )

      {

      //rev is greater the last revsion number and revInDataBase isn't -1

      // it is a updated data file

      else if (userSpecifyRev>revInDataBase && revInDataBase>0)

      {

        //archive the old entry

      else if ( userSpecifyRev < revInDataBase && revInDataBase > 0)

      {

        throw new Exception("Local server: "+MetaCatUtil.getOption("server")+

                 " has newer revision of doc: "+docIdWithoutRev+"."

                  +revInDataBase+". Please notify it.");

      }

      else

      {

        throw new Exception("Revision number couldn't be "

                    +userSpecifyRev);

      }

      String docid = ac.getDocid();

      String rev = ac.getRev();

      String dateString = formatter.format(localtime);

      String sqlDateString = dbAdapter.getDateTimeFunction();

      {

        sql.append("insert into xml_documents (docid, docname, doctype, ");

        sql.append("user_owner, user_updated, server_location, rev,date_created");

        sql.append(", date_updated, public_access) values ('");

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

        sql.append(docname).append("','");

        sql.append(doctype).append("','");

        sql.append(user).append("','");

        sql.append(user).append("','");

        sql.append(serverCode).append("','");

        sql.append(rev).append("',");

        sql.append(sqlDateString).append(",");

        sql.append(sqlDateString).append(",");

        sql.append("'0')");

      }

      else if (action != null && action.equals("update"))

      {

        sql.append("update xml_documents set docname ='");

        sql.append(docname).append("', ");

        sql.append("user_updated='");

        sql.append(user).append("', ");

        sql.append("server_location='");

        sql.append(serverCode).append("',");

        sql.append("rev='");

        sql.append(rev).append("',");

        sql.append("date_updated=");

        sql.append(sqlDateString);

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

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

      }

      dbconn.setAutoCommit(false);

      dbconn.commit();

    finally

    {

      dbconn.setAutoCommit(true);

      DBConnectionPool.returnDBConnection(dbconn, serialNumber);

  }

   * @param  input, the input stream which contain the file content.

   * @param  , the input stream which contain the file content

   * @param docname - the name of DTD, for data file, it is a docid number.

   * @param doctype - "BIN" for data file

   * @param accnum the accession number to use for the INSERT OR UPDATE, which

   *               includes a revision number for this revision of the document

   *               (e.g., knb.1.1)

   * @param user the user that owns the document

   * @param notificationServer, the server to notify force replication info to

   *                            local metacat

                 String filePath, String docname, String doctype, String accnum,

                   String user, String docHomeServer, String notificationServer)

 {

    {

      throw new

            Exception("Please specify the directory where file will be store");

    }

    if (accnum==null||accnum.equals(""))

    {

      throw new Exception("Please specify the stored file name");

    }

    // xml_replication table

    //serverList.addToServerListIfItIsNot(docHomeServer);

    insertServerIntoReplicationTable(docHomeServer);

    // Get server code again

    serverCode = getServerCode(docHomeServer);

    //register data file into xml_documents table

    registerDocumentInReplication(docname, doctype, accnum, user, serverCode);

    //write inputstream into file system.

    File dataDirectory = new File(filePath);

    File newFile = new File(dataDirectory, accnum);

    // that uses a default-sized output buffer

    FileOutputStream fos = new FileOutputStream(newFile);

    BufferedOutputStream outPut = new BufferedOutputStream(fos);

    bis = new BufferedInputStream(input);

    byte[] buf = new byte[4 * 1024]; // 4K buffer

    int b = bis.read(buf);

    {

        b = bis.read(buf);

    bis.close();

	  outPut.close();

	  fos.close();

    // Force replicate data file

    ForceReplicationHandler forceReplication = new ForceReplicationHandler

                                    (accnum, false, notificationServer);

  public static boolean getDataFileLockGrant(String accnum)

                                                  throws Exception

  {

    {

      int serverLocation=getServerLocationNumber(accnum);

    }

    catch (Exception e)

    {

    }

   * If server code is 1, it get.

   * If server code is not 1 but call replication getlock successfully,

   * it get

   * else, it didn't get

   * @param accnum, the ID of the document

   * @param action, the action to the document

   * @param serverCode, the server location code

   */

  public static boolean getDataFileLockGrant(String accnum, int serverCode)

                                          throws Exception

  {

    boolean flag=true;

    String docid = MetaCatUtil.getDocIdFromString(accnum);

    int rev = MetaCatUtil.getVersionFromString(accnum);

    if (serverCode == 1)

    {

      flag=true;

      return flag;

    }

    //if((serverCode != 1 && action.equals("UPDATE")) )

    if (serverCode != 1)

    { //if this document being written is not a resident of this server then

      //we need to try to get a lock from it's resident server.  If the

      //resident server will not give a lock then we send the user a message

      //saying that he/she needs to download a new copy of the file and

      //merge the differences manually.

        MetaCatUtil.getLocalReplicationServerName()+"&action=getlock&updaterev="

      //System.out.println("sending message: " + u.toString());

      String serverResStr = MetacatReplication.getURLContent(u);

      String openingtag =serverResStr.substring(0, serverResStr.indexOf(">")+1);

      if(openingtag.equals("<lockgranted>"))

      {

        //the lock was granted go ahead with the insert

        //System.out.println("In lockgranted");

        MetacatReplication.replLog("lock granted for " + accnum + " from " +

                                      server);

        flag=true;

        return flag;

      }//if

      else if(openingtag.equals("<filelocked>"))

      {//the file is currently locked by another user

       //notify our user to wait a few minutes, check out a new copy and try

       //again.

        //System.out.println("file locked");

        MetacatReplication.replLog("lock denied for " + accnum + " on " +

                                   server + " reason: file already locked");

        throw new Exception("The file specified is already locked by another " +

                            "user.  Please wait 30 seconds, checkout the " +

                            "newer document, merge your changes and try " +

                            "again.");

      }

      else if(openingtag.equals("<outdatedfile>"))

      {//our file is outdated.  notify our user to check out a new copy of the

       //file and merge his version with the new version.

        //System.out.println("outdated file");

        MetacatReplication.replLog("lock denied for " + accnum + " on " +

                                    server + " reason: local file outdated");

        throw new Exception("The file you are trying to update is an outdated" +

                            " version.  Please checkout the newest document, " +

                            "merge your changes and try again.");

      }//else if

    }//if

   return flag;

  }//getDataFileLockGrant

  /**

   */

  public String getDocname() {

    return docname;

  }

  /**

   * get the document type (which is the PublicID)

   */

  public String getDoctype() {

    return doctype;

  }

  /**

   * get the system identifier

   */

  public String getSystemID() {

    return system_id;

  }

  /**

   * get the root node identifier

   */

  public long getRootNodeID() {

    return rootnodeid;

  }

  /**

   * get the creation date

   */

  public String getCreateDate() {

    return createdate;

  }

  /**

   * get the update date

   */

  public String getUpdateDate() {

    return updatedate;

  }

   * Get the document identifier (docid)

   */

  public String getDocID() {

    return docid;

  }

//  /**

//   *get the document title

//   */

//  public String getDocTitle() {

//    return doctitle;

//  }

  public String getUserowner() {

    return userowner;

  }

  public String getUserupdated() {

    return userupdated;

  }

  public int getServerlocation() {

    return serverlocation;

  }

    return docHomeServer;