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.io.BufferedOutputStream;

import java.io.StringWriter;

import java.io.Writer;

import java.sql.PreparedStatement;

import java.sql.ResultSet;

import java.sql.SQLException;

import org.xml.sax.DTDHandler;

import org.xml.sax.EntityResolver;

import org.xml.sax.ErrorHandler;

import org.xml.sax.InputSource;

import org.xml.sax.helpers.XMLReaderFactory;

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

 * text document to a database connection using SAX.

{

    /* Constants */

    public static final String SCHEMA = "Schema";

    public static final String DTD = "DTD";

    public static final String EML200 = "eml200";

    public static final String EML210 = "eml210";

    public static final String EXTERNALSCHEMALOCATIONPROPERTY = "http://apache.org/xml/properties/schema/external-schemaLocation";

     * public static final String EXTERNALSCHEMALOCATION =

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

     * http://dev.nceas.ucsb.edu/tao/schema/eml.xsd"+ "

     * http://www.xml-cml.org/schema/stmml

     * http://dev.nceas.ucsb.edu/tao/schema/stmml.xsd";

     */

    public static final String DECLARATIONHANDLERPROPERTY = "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";

    public static final String EML2_1_0NAMESPACE = MetaCatUtil

            .getOption("eml2_1_0namespace");

    // "eml://ecoinformatics.org/eml-2.1.0";

    public static final String EML2_0_1NAMESPACE = MetaCatUtil

            .getOption("eml2_0_1namespace");

    // "eml://ecoinformatics.org/eml-2.0.1";

    public static final String EML2_0_0NAMESPACE = MetaCatUtil

            .getOption("eml2_0_0namespace");

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

    public static final String DOCNAME = "docname";

    public static final String PUBLICID = "publicid";

    public static final String SYSTEMID = "systemid";

    static final int ALL = 1;

    static final int WRITE = 2;

    static final int READ = 4;

    private static final AbstractDatabase dbAdapter = MetaCatUtil.dbAdapter;

    private DBConnection connection = null;

    private String docid = null;

    private String updatedVersion = null;

    private String docname = null;

    private String doctype = null;

    private String validateType = null; //base on dtd or schema

    private String createdate = null;

    private String updatedate = null;

    private String system_id = null;

    private String userowner = null;

    private String userupdated = null;

    private int rev;

    private int serverlocation;

    private String docHomeServer;

    private String publicaccess;

    private long rootnodeid;

    private ElementNode rootNode = null;

    private TreeSet nodeRecordList = null;

     * Constructor used to create a document and read the document information

     * 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).

     *            the database connection from which to read the document

     * @param docid

     *            the identifier of the document to be created

     * @param readNodes

     *            flag indicating whether the xmlnodes should be read

     */

    public DocumentImpl(String docid, boolean readNodes) throws McdbException

    {

        try {

            //this.conn = conn;

            this.docid = docid;

            getDocumentInfo(docid);

                // Download all of the document nodes using a single SQL query

                // 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) {

    }

     * Constructor, creates document from database connection, used for reading

     * the document

     *            the database connection from which to read the document

     * @param docid

     *            the identifier of the document to be created

     */

    public DocumentImpl(String docid) throws McdbException

    {

        this(docid, true);

     * 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.

     * 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

     *            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.

    public DocumentImpl(DBConnection conn, long rootNodeId, String docName,

            String docType, String docId, String newRevision, String action,

            String user, String pub, String catalogId, int serverCode)

            throws SQLException, Exception

        this.rootnodeid = rootNodeId;

        this.docname = docName;

        this.doctype = docType;

        this.docid = docId;

        this.updatedVersion = newRevision;

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

    /**

     * This method will be call in handleUploadRequest in MetacatServlet class

     */

    public static void registerDocument(String docname, String doctype,

            // get server location for this doc

            int serverLocation = getServerLocationNumber(accnum);

                             serverLocation);

            throw e;

        }

     * 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

     * class only be called in MetaCatServerlet.

     *            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

     *            the groups that owns the document

     *            the serverid from xml_replication on which this document

     *            resides.

     */

    public static void registerDocument(String docname, String doctype,

            throws SQLException, AccessionNumberException, Exception

        int serialNumber = -1;

        PreparedStatement pstmt = null;

        //MetaCatUtil util = new MetaCatUtil();

        AccessionNumber ac;

        String action = null;

        try {

            //dbconn = util.openDBConnection();

            //check out DBConnection

            dbconn = DBConnectionPool

                    .getDBConnection("DocumentImpl.registerDocument");

            serialNumber = dbconn.getCheckOutSerialNumber();

            String docIdWithoutRev = MetaCatUtil.getDocIdFromString(accnum);

            int userSpecifyRev = MetaCatUtil.getVersionFromString(accnum);

            int revInDataBase = getLatestRevisionNumber(docIdWithoutRev);

            //revIndataBase=-1, there is no record in xml_documents table

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

            //user specified rev should be great than 0

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

                ac = new AccessionNumber(accnum, "insert");

                action = "insert";

            }

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

            // it is a updated data file

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

                   "User " + user

                   + " does not have permission to update the document"

                   + accnum); }

                archiveDocRevision(docIdWithoutRev, user);

                //delete the old entry in xml_documents

                //deleteXMLDocuments(docIdWithoutRev);

                ac = new AccessionNumber(accnum, "update");

                action = "update";

            }

            //other situation

            else {

                        + userSpecifyRev);

            }

            String docid = ac.getDocid();

            String rev = ac.getRev();

            /*

             * SimpleDateFormat formatter = new SimpleDateFormat ("MM/dd/yy

             * HH:mm:ss"); Date localtime = new Date(); String dateString =

             * formatter.format(localtime); String

             * sqlDateString=dbAdapter.toDate(dateString, "MM/DD/YY

             * HH24:MI:SS");

             */

            String sqlDateString = dbAdapter.getDateTimeFunction();

            if (action != null && action.equals("insert")) {

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

            pstmt.execute();

            pstmt.close();

            //dbconn.close();

        } finally {

            try {

                    pstmt.close();

                }

                DBConnectionPool.returnDBConnection(dbconn, serialNumber);

            }

        }

     * (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.

     *            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

    {

        DBConnection dbconn = null;

        int serialNumber = -1;

        //MetaCatUtil util = new MetaCatUtil();

        AccessionNumber ac;

        PreparedStatement pstmt = null;

        String action = null;

        try {

            //dbconn = util.openDBConnection();

            dbconn = DBConnectionPool.getDBConnection(

                    "DocumentImpl.registerDocumentInReplication");

            serialNumber = dbconn.getCheckOutSerialNumber();

            String docIdWithoutRev = MetaCatUtil

                    .getDocIdFromAccessionNumber(accnum);

            int userSpecifyRev = MetaCatUtil

                    .getRevisionFromAccessionNumber(accnum);

            int revInDataBase = getLatestRevisionNumber(docIdWithoutRev);

            //revIndataBase=-1, there is no record in xml_documents table

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

            //user specified rev should be great than 0

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

                ac = new AccessionNumber(accnum, "insert");

                action = "insert";

            }

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

            // it is a updated data file

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

                archiveDocRevision(docIdWithoutRev, user);

                //delete the old entry in xml_documents

                //deleteXMLDocuments(docIdWithoutRev);

                ac = new AccessionNumber(accnum, "update");

                action = "update";

            }

            // local server has newer version, then notify the remote server

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

                throw new Exception("Local server: "

                        + MetaCatUtil.getOption("server")

                        + " has newer revision of doc: " + docIdWithoutRev

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

            }

            //other situation

            else {

                        + userSpecifyRev);

            }

            String docid = ac.getDocid();

            String rev = ac.getRev();

            /*

             * SimpleDateFormat formatter = new SimpleDateFormat ("MM/dd/yy

             * HH:mm:ss"); Date localtime = new Date(); String dateString =

             * formatter.format(localtime); String

             * sqlDateString=dbAdapter.toDate(dateString, "MM/DD/YY

             * HH24:MI:SS");

             */

            String sqlDateString = dbAdapter.getDateTimeFunction();

            if (action != null && action.equals("insert")) {

                sql.append("insert into xml_documents (docid, docname, " +

                           "doctype, ");

                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("'");

            }

            // Set auto commit fasle

            dbconn.setAutoCommit(false);

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

            // Commit the insert

            dbconn.commit();

            pstmt.close();

            //dbconn.close();

        } finally {

            // Set DBConnection auto commit true

            dbconn.setAutoCommit(true);

            pstmt.close();

            DBConnectionPool.returnDBConnection(dbconn, serialNumber);

        }

     * This method will register a data file entry in xml_documents and save a

     * data file input Stream into file system.. It is only used in replication

     *            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 docHomeServer,

     *            the home server of the docid

     * @param notificationServer,

     *            the server to notify force replication info to local metacat

     */

    public static void writeDataFileInReplication(InputStream input,

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

            String user, String docHomeServer, String notificationServer)

            throws SQLException, AccessionNumberException, 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);

        serverCode = getServerCode(docHomeServer);

        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);

            outPut.write(buf, 0, b);

            b = bis.read(buf);

        }

        bis.close();

        outPut.close();

        fos.close();

        ForceReplicationHandler forceReplication = new ForceReplicationHandler(

                accnum, false, notificationServer);

    }

     * Get a lock for a given document.

     */

    public static boolean getDataFileLockGrant(String accnum) throws Exception

            int serverLocation = getServerLocationNumber(accnum);

            return getDataFileLockGrant(accnum, serverLocation);

        } catch (Exception e) {

            throw e;

        }

     * The method will check if metacat can get data file lock grant 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

     *            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;

        //MetaCatUtil util = new MetaCatUtil();

        String docid = MetaCatUtil.getDocIdFromString(accnum);

        int rev = MetaCatUtil.getVersionFromString(accnum);

            flag = true;

            return flag;

        }

        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.

                    .getServerNameForServerCode(serverCode);

            MetacatReplication.replLog("attempting to lock " + accnum);

            URL u = new URL("https://" + server + "?server="

                    + MetaCatUtil.getLocalReplicationServerName()

                    + "&action=getlock&updaterev=" + rev + "&docid=" + docid);

            //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

                                                         // 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.");

            }

        }

        return flag;

    }

     * get the document name

     */

    public String getDocname()

    }

     * 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()

    }

     * 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()