Metacat

package edu.ucsb.nceas.metacat;

import java.io.BufferedInputStream;

import java.io.File;

import java.io.FileInputStream;

import java.io.FileReader;

import org.apache.log4j.Logger;

import org.apache.log4j.PropertyConfigurator;

import au.com.bytecode.opencsv.CSVWriter;

				Enumeration<String> paramlist =(Enumeration<String>)request.getParameterNames();

				while (paramlist.hasMoreElements()) {

					value = request.getParameterValues(name);

					// Decode the docid and mouse click information

					return;

				}

				logMetacat.info("Action is: " + action);

				// This block handles session management for the servlet

			dq = new DataQuery();

		}

    	ResultSet rs = null;

		try {

			cm = new CartManager();

		}

    	if (field != null && path != null) {

    		fields.put(field[0], path[0]);

    	}

        /*

		 * Perform spatial query against spatial cache

		 */

        SpatialQuery sq = new SpatialQuery();

        Vector<String> docids = sq.filterByBbox( _xmin, _ymin, _xmax, _ymax );

        // logMetacat.info(" --- Spatial Query completed. Passing on the SQuery

		 */

        String[] qformatArray = new String[1];

        try {

            qformatArray[0] = _skin;

        } catch (java.lang.NullPointerException e) {

            // should be "default" but keep this for backwards compatibility

            return;

        }

        logMetacat.info("user " + un + " is trying to login");

        String qformat = "xml";

        if(params.get("qformat") != null){

        }

        try {

        Logger logMetacat = Logger.getLogger(MetaCatServlet.class);

        String qformat = "xml";

        if(params.get("qformat") != null){

        }

        // close the connection

     * @param response the response object linked to the client

     * @param conn the database connection

     */

            HttpServletResponse response, String user, String[] groups,

            String sessionid) throws PropertyNotFoundException {

        double startTime = System.currentTimeMillis() / 1000;

        try {

            // read the params

            if (params.containsKey("docid")) {

            }

            // Create a DBuery to handle export

            queryObj = new DBQuery();

     * @param user the username sent the request

     * @param groups the user's groupnames

     */

            HttpServletRequest request, HttpServletResponse response,

            String user, String passWord, String[] groups) {

        Logger logMetacat = Logger.getLogger(MetaCatServlet.class);

        try {

            // read the params

            if (params.containsKey("inlinedataid")) {

            }

            // Get the docid

            inlineDataId = docs[0];

            } else {

                //check data access level

                try {

                            PermissionController.getUnReadableInlineDataIdList(docId,

                            user, groups, false);

                    String inlineDataIdWithoutRev = MetaCatUtil.getInlineDataIdWithoutRev(inlineDataId);

        }

    }

    /**

     * Handle the "read" request of metadata/data files from Metacat or any

     * @param user the username sent the request

     * @param groups the user's groupnames

     */

            HttpServletResponse response, String user, String passWord,

            String[] groups) {

        Logger logMetacat = Logger.getLogger(MetaCatServlet.class);

            // read the params

            if (params.containsKey("docid")) {

            }

            if (params.containsKey("qformat")) {

            }

            // the param for only metadata (eml)

            // we don't support read a eml document without inline data now.

            for (int i = 0; i < docs.length; i++) {

            	String providedFileName = null;

            	if (params.containsKey(docs[i])) {

                }

                try {

                    URL murl = new URL(docs[i]);

                            murl.getQuery());

                    // case docid="http://.../?docid=aaa"

                    // or docid="metacat://.../?docid=bbb"

                    if (murlQueryStr.containsKey("docid")) {

                        // get only docid, eliminate the rest

                        if (zip) {

                            addDocToZip(request, docid, providedFileName, zout, user, groups);

                        } else {

    private void readFromMetacat(HttpServletRequest request,

            HttpServletResponse response, String docid, String qformat,

            String abstrpath, String user, String[] groups, boolean zip,

            throws ClassNotFoundException, IOException, SQLException,

            McdbException, Exception {

    	String documentDir = PropertyService.getProperty("application.documentfilepath");

     * database connection

     */

    private void handleInsertOrUpdateAction(HttpServletRequest request,

            String user, String[] groups) {

        Logger logMetacat = Logger.getLogger(MetaCatServlet.class);

        DBConnection dbConn = null;

        String qformat = null;

        if(params.containsKey("qformat"))

        {

        }

        if(params.get("docid") == null){

            // Get the document indicated

            System.out.println("params: " + params.toString());

            String pub = null;

            if (params.containsKey("public")) {

            }

            StringReader dtd = null;

            if (params.containsKey("dtdtext")) {

                try {

                    if (!dtdtext[0].equals("")) {

                        dtd = new StringReader(dtdtext[0]);

                            // set eml2 base	 validation parser

                            String rule = DocumentImpl.EML200;

                            // using emlparser to check id validation

                            documentWrapper = new DocumentImplWrapper(rule, true);

                        } else if (namespace.compareTo(

                                DocumentImpl.EML2_1_0NAMESPACE) == 0) {

                            // set eml2 base validation parser

                            String rule = DocumentImpl.EML210;

                            // using emlparser to check id validation

                            documentWrapper = new DocumentImplWrapper(rule, true);

                        } else {

                            // set schema base validation parser

                    }

                }

                String newdocid = null;

                String doAction = null;

    throws IOException {

        Logger logMetacat = Logger.getLogger(MetaCatServlet.class);

        StringBuffer cbuff = new StringBuffer();

        boolean validate = false;

        boolean commented = false;

        int c;

        // check the stack whether it contains the keywords:

        // "<!DOCTYPE", "PUBLIC" or "SYSTEM", and ">" in this order

        if (st.size() == 4) {

                validate = true && !commented;

            }

        }

     * Handle the database delete request and delete an XML document from the

     * database connection

     */

            HttpServletRequest request, HttpServletResponse response,

            String user, String[] groups) {

        Logger logMetacat = Logger.getLogger(MetaCatServlet.class);

        if(docid == null){

            response.setContentType("text/xml");

    /**

     * Handle the validation request and return the results to the requestor

     */

        // Get the document indicated

        String valtext = null;

        int serialNumber = -1;

        try {

        } catch (Exception nullpe) {

            String docid = null;

            try {

                // Find the document id number

                // Get the document indicated from the db

                DocumentImpl xmldoc = new DocumentImpl(docid);

                    .getDBConnection("MetaCatServlet.handleValidateAction");

            serialNumber = dbConn.getCheckOutSerialNumber();

            DBValidate valobj = new DBValidate(dbConn);

            // set content type and other response header fields first

     * "rev;doctype"

     */

    private void handleGetRevisionAndDocTypeAction(PrintWriter out,

        // To store doc parameter

        String[] docs = new String[10];

        // Store a single doc id

        String givenDocId = null;

        // Get docid from parameters

        if (params.containsKey("docid")) {

        }

        // Get first docid form string array

        givenDocId = docs[0];

     * connection in XML format

     */

    private void handleGetAccessControlAction(PrintWriter out,

            String[] groupnames) {

        DBConnection dbConn = null;

        int serialNumber = -1;

        try {

     * Handle "getdoctypes" action. Read all doctypes from db connection in XML

     * format

     */

            HttpServletResponse response) {

        try {

            DBUtil dbutil = new DBUtil();

     * Handle the "getdtdschema" action. Read DTD or Schema file for a given

     * doctype from Metacat catalog system

     */

            HttpServletResponse response) {

        String doctype = null;

        // get only the first doctype specified in the list of doctypes

        // it could be done for all doctypes in that list

        if (doctypeArr != null) {

        }

        try {

    }

            HttpServletResponse response) {

        String id = null;

        boolean exists = false;

        if(params.get("docid") != null) {

        }

        try {

     * Handle the "getalldocids" action. return a list of all docids registered

     * in the system

     */

            HttpServletResponse response) {

        String scope = null;

        if(params.get("scope") != null) {

        }

        try {

            DBUtil dbutil = new DBUtil();

            out.println("<?xml version=\"1.0\"?>");

            out.println("<idList>");

            out.println("  <scope>" + scope + "</scope>");

            for(int i=0; i<docids.size(); i++) {

                out.println("  <docid>" + docid + "</docid>");

            }

            out.println("</idList>");

     * Handle the "getlastdocid" action. Get the latest docid with rev number

     * from db connection in XML format

     */

            HttpServletResponse response) {

        if (scope == null) {

        }

        try {

     * @param request the http request object for getting request details

     * @param response the http response object for writing output

     */

            HttpServletResponse response, String username, String[] groups) {

        Logger logMetacat = Logger.getLogger(MetaCatServlet.class);

        try {

            }

            // Get all of the parameters in the correct formats

            String start = null;

            String end = null;

            if (startArray != null) {

	 * @param username

	 *            the username of the authenticated user

	 */

            HttpServletRequest request, HttpServletResponse response,

            String username, String[] groups) {

        Logger logMetacat = Logger.getLogger(MetaCatServlet.class);

        // Get all of the parameters in the correct formats

        // Rebuild the indices for appropriate documents

        try {

            if (docid == null || docid.length == 0) {

                // Process all of the documents

                try {

                    while (it.hasNext()) {

                        buildDocumentIndex(id, out);

                    }

                } catch (SQLException se) {

        // Parse the multipart form, and save the parameters in a Hashtable and

        // save the FileParts in a hashtable

        int sizeLimit = 1000;

        try {

        	sizeLimit = 

                if (part.isParam()) {

                    // it's a parameter part

                    ParamPart paramPart = (ParamPart) part;

                    if (name.equals("action")) {

                    }

                } else if (part.isFile()) {

                    // it's a file part

     */

    private void handleInsertMultipartAction(HttpServletRequest request, 

            HttpServletResponse response,

            String username, String[] groupnames)

    {

      Logger logMetacat = Logger.getLogger(MetaCatServlet.class);

      if (params.containsKey("docid")) 

      {

      }

      if(params.containsKey("qformat")) 

      {

      }

      // Make sure we have a docid and datafile

        logMetacat.info("Uploading data docid: " + docid);

        // Get a reference to the file part of the form

        //FilePart filePart = (FilePart) fileList.get("datafile");

        System.out.println("filename: " + fileName);

        logMetacat.info("Uploading filename: " + fileName);

        // Check if the right file existed in the uploaded data

              File dataDirectory = new File(datafilepath);

              dataDirectory.mkdirs();

              File newFile = null;

              String newFileName = dataDirectory + File.separator + docid;

              long size = 0;

              boolean fileExists = false;

                  numread = fr.read(c, 0, 1024);

                }

                while(keys.hasMoreElements())

                { //convert the params to arrays

                  String[] s = new String[1];

                  params.put(key, s);

                }

                //add the doctext to the params

     * registering it in the Metacat db

     */

    private void handleUploadAction(HttpServletRequest request,

            String username, String[] groupnames, HttpServletResponse response) {

        Logger logMetacat = Logger.getLogger(MetaCatServlet.class);

        //PrintWriter out = null;

        //Connection conn = null;

        String docid = null;

        String qformat = null;

        String output = "";

         */

        if (params.containsKey("docid")) {

        }

        if(params.containsKey("qformat")) {

        }

        // Make sure we have a docid and datafile

            logMetacat.info("Uploading data docid: " + docid);

            // Get a reference to the file part of the form

            //FilePart filePart = (FilePart) fileList.get("datafile");

            logMetacat.info("Uploading filename: " + fileName);

            // Check if the right file existed in the uploaded data

            if (fileName != null) {

                        File dataDirectory = new File(datafilepath);

                        dataDirectory.mkdirs();

                        File newFile = null;

                        String newFileName = dataDirectory + File.separator + docid;

                        long size = 0;

                        boolean fileExists = false;

                        // not get force replication info from another metacat

                        ForceReplicationHandler frh = new ForceReplicationHandler(

                                docid, "insert", false, null);

                        // set content type and other response header fields

                        // first

    /*

     * A method to handle set access action

     */

            String username) {

        Logger logMetacat = Logger.getLogger(MetaCatServlet.class);

        String[] docList = null;

        String permission = null;

        String permType = null;

        String permOrder = null;

        String error = null;

        String success = null;

        boolean isEmlPkgMember = false;

        // Get parameters

        if (params.containsKey("docid")) {

        }

        if (params.containsKey("principal")) {

        }

        if (params.containsKey("permission")) {

        }

        if (params.containsKey("permType")) {

        }

        if (params.containsKey("permOrder")) {

        }

        }

        // Get package doctype set

        try {

        	packageSet = 

        		MetaCatUtil.getOptionList(PropertyService.getProperty("xml.packagedoctypeset"));

        if (packageSet != null) {

            for (int i = 0; i < packageSet.size(); i++) {

                logMetacat.debug("doctype in package set: "

            }

        }

            }

            ForceReplicationHandler frh = 

            	new ForceReplicationHandler(accessionNumber, isXml, null);

        }

        outputResponse(successList, errorList, out);

            pstmt.execute();

            rs = pstmt.getResultSet();

            boolean hasRow = rs.next();

            if (hasRow) {

                fieldValue = rs.getString(1);

            } else {

     *

     * @ returns the array of identifiers

     */

        Logger logMetacat = Logger.getLogger(MetaCatServlet.class);

        PreparedStatement pstmt = null;

        ResultSet rs = null;

        DBConnection conn = null;

    /*

     * A method to output setAccess action result

     */

            PrintWriter out) {

        boolean error = false;

        boolean success = false;

        if (successList != null) {

            for (int i = 0; i < successList.size(); i++) {

                out.println(SUCCESS);

                out.println(SUCCESSCLOSE);

                success = true;

            }

        if (errorList != null) {

            for (int i = 0; i < errorList.size(); i++) {

                out.println(ERROR);

                out.println(ERRORCLOSE);

                error = true;

            }

     * append rev for it. The rev come from xml_documents

     */

    private static String appendRev(String docid) throws Exception {

        String newAccNum = null;

        String separator = PropertyService.getProperty("document.accNumSeparator");

        int firstIndex = docid.indexOf(separator);