Metacat

	 * Test insert a xml document successfully

	 */

	public void testInsertXMLDocument() throws PropertyNotFoundException {

		logMetacat.info("insert docid: " + name);

		String content = "<?xml version=\"1.0\"?>"

				+ "<!DOCTYPE acl PUBLIC \"-//ecoinformatics.org//"

	 * In the String, there is no <!Doctype ... Public/System/>

	 */

	public void testInsertInvalidateXMLDocument() throws PropertyNotFoundException  {

		logMetacat.info("insert docid: " + name);

		String content = "<?xml version=\"1.0\"?>"

				+ "<acl authSystem=\"knb\" order=\"allowFirst\">" + "<identifier>" + name

	 * There is no </acl> in this string

	 */

	public void testInsertNonWellFormedXMLDocument() throws PropertyNotFoundException  {

		logMetacat.info("insert non well-formed docid: " + name);

		String content = "<?xml version=\"1.0\"?>"

				+ "<acl authSystem=\"knb\" order=\"allowFirst\">" + "<identifier>" + name

	 * Test read a xml document  in xml format successfully

	 */

	public void testReadXMLDocumentXMLFormat() throws PropertyNotFoundException  {

		assertTrue(handleReadAction(name, "xml"));

	}

	 * Test read a xml document  in html format successfully

	 */

	public void testReadXMLDocumentHTMLFormat() throws PropertyNotFoundException {

		assertTrue(handleReadAction(name, "html"));

	}

	 * Test read a xml document  in zip format successfully

	 */

	public void testReadXMLDocumentZipFormat() throws PropertyNotFoundException {

		assertTrue(handleReadAction(name, "zip"));

	}

	 * Test insert a xml document successfully

	 */

	public void testUpdateXMLDocument() throws PropertyNotFoundException {

		logMetacat.info("update docid: " + name);

		String content = "<?xml version=\"1.0\"?>"

				+ "<!DOCTYPE acl PUBLIC \"-//ecoinformatics.org//"

	 * Test insert a data file successfully

	 */

	public void testInertDataFile() throws PropertyNotFoundException {

		logMetacat.info("insert data file docid: " + name);

		logMetacat.info("insert data file ");

		File hello = new File("test/jones.204.22.xml");

	 * Test delete a xml document successfully

	 */

	public void testDeleteXMLDocument() throws PropertyNotFoundException {

		logMetacat.info("delete docid: " + name);

		assertTrue(handleDeleteFile(name));

            System.out.println("---- SQL ------------------");

            QuerySpecification qspec = new QuerySpecification(xml, 

                    PropertyService.getProperty("saxparser"), 

            String query = qspec.printSQL(false);

           assertTrue(selectionQuery.equals(query.trim()));

        } catch (IOException e) {

            System.out.println("---- orginal EXT SQL  ------------------\n"+extendedQuery);

            QuerySpecification qspec = new QuerySpecification(xml, 

                    PropertyService.getProperty("saxparser"), 

            String query = 

                    qspec.printExtendedSQL(

                            "'obfs.45337', 'obfs.45338', 'obfs.45346'", true);

        	String   createDate = result.getString(5);

        	String updateDate = result.getString(6);

        	String completeDocid = docid

            completeDocid += rev;

            // Put everything into a string buffer

            StringBuffer document = new StringBuffer();

	public void testInsertXMLDocument() {

		String name = null;

		try {

		} catch (PropertyNotFoundException pnfe) {

			fail("Could not find property: " + pnfe.getMessage());

		}

	public void testInsertInvalidateXMLDocument() {

		String name = null;

		try {

		} catch (PropertyNotFoundException pnfe) {

			fail("Could not find property: " + pnfe.getMessage());

		}

	public void testInsertNonWellFormedXMLDocument() {

		String name = null;

		try {

		} catch (PropertyNotFoundException pnfe) {

			fail("Could not find property: " + pnfe.getMessage());

		}

	public void testReadXMLDocumentXMLFormat() {

		String name = null;

		try {

		} catch (PropertyNotFoundException pnfe) {

			fail("Could not find property: " + pnfe.getMessage());

		}

	public void testReadXMLDocumentHTMLFormat() {

		String name = null;

		try {

		} catch (PropertyNotFoundException pnfe) {

			fail("Could not find property: " + pnfe.getMessage());

		}	

	public void testReadXMLDocumentZipFormat() {

		String name = null;

		try {

		} catch (PropertyNotFoundException pnfe) {

			fail("Could not find property: " + pnfe.getMessage());

		}	

	public void testUpdateXMLDocument() {

		String name = null;

		try {

		} catch (PropertyNotFoundException pnfe) {

			fail("Could not find property: " + pnfe.getMessage());

		}		

	public void testDeleteXMLDocument() {

		String name = null;

		try {

		} catch (PropertyNotFoundException pnfe) {

			fail("Could not find property: " + pnfe.getMessage());

		}

			// schema, which accidentily points to wrong version of

			// eml-resource.xsd.

			String correctedEML201Doc = PropertyService

			if (correctedEML201Doc != null && correctedEML201Doc.equals(FALSE)) {

				logMetacat.info("===Start to correct eml201 documents");

				EML201DocumentCorrector correct = new EML201DocumentCorrector();

				boolean success = correct.run();

				if (success) {

				}

				logMetacat.info("====Finish to correct eml201 documents");

			}

    private static String appendRev(String docid) throws Exception {

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

        String newAccNum = null;

        int firstIndex = docid.indexOf(separator);

        int lastIndex = docid.lastIndexOf(separator);

        if (firstIndex == lastIndex) {

    // create xml document

    try

    {

                    DBUtil.getLatestRevisionInDocumentTable(eml2DocId);

      //System.out.println("the acc number is !!!!!!!!!!!!!!!!!"+accNumber);

      xmlDoc = new DocumentImpl(accNumber);

    String xmlDoc = null;

    try

    {

        DBUtil.getLatestRevisionInDocumentTable(physicalDocid);

      //System.out.println("the accenumber is !!!!!!!!!!!!!!!!!!" + accNumber);

      DocumentImpl doc = new DocumentImpl(accNumber);

                int thisrev = DBUtil.getLatestRevisionInDocumentTable(docid);

                logMetacat.info("this revsion is: " + thisrev);

                // Save the old document publicaccessentry in a backup table

                thisdoc = new DocumentImpl(accNumber, false);

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

                logMetacat.info("after archiveDoc");

        ForceReplicationHandler frh = new ForceReplicationHandler(accnum,

                action, true, null);

        // clear cache after inserting or updating a document

        {

          //System.out.println("the string stored into cache is "+ resultsetBuffer.toString());

     	   DBQuery.clearQueryResultCache();

        }

        // clear cache after inserting or updating a document

        {

          //System.out.println("the string stored into cache is "+ resultsetBuffer.toString());

     	   DBQuery.clearQueryResultCache();

            ForceReplicationHandler frh = new ForceReplicationHandler(

                             accnum, ForceReplicationHandler.DELETE, isXML, notifyServer);

            // clear cache after inserting or updating a document

            {

              //System.out.println("the string stored into cache is "+ resultsetBuffer.toString());

         	   DBQuery.clearQueryResultCache();

        try {

            if (doc == null) {

                DBUtil.getLatestRevisionInDocumentTable(docid);

                    doc = new DocumentImpl(accNumber);

            }

      String createdDate = (String)docinfoHash.get("date_created");

      String updatedDate = (String)docinfoHash.get("date_updated");

      //docid should include rev number too

                                              (String)docinfoHash.get("rev");*/

      logMetacat.info("docid in repl: "+accNumber);

      String docType = (String)docinfoHash.get("doctype");

      String createdDate = (String)docinfoHash.get("date_created");

      String updatedDate = (String)docinfoHash.get("date_updated");

      //docid should include rev number too

                                              (String)docinfoHash.get("rev");*/

         //because delete method docid should have rev number

         //so we just add one for it. This rev number is no sence.

         //System.out.println("accnum: "+accnum);

         DocumentImpl.delete(accnum, null, null, notifyServer);

         logMetacat.info("Successfully deleted doc " + docId);

         }

       }

       // this is non-data file

       if(flag && !dataFile)

       {

           flag = true;    

       }

       // this is non-data file

       if(flag && !dataFile)

       {

				rev = rs.getInt(2);

				String sep = ".";

				try {

				} catch (PropertyNotFoundException pnfe) {

					logMetacat.error("Could not find account separator.  Setting to '.': " + pnfe.getMessage());

				}

	 */

	private AccessionNumber() throws AccessionNumberException {

		try {

		} catch (PropertyNotFoundException pnfe) {

			throw new AccessionNumberException("Could not retrieve property "

					+ "in constructor: " + pnfe.getMessage());

    String accnum = null;

    String sep = ".";

    try {

    } catch (PropertyNotFoundException pnfe) {

    	logMetacat.error("could not get property 'accNumSeparator'.  setting to '.': " 

    			+ pnfe.getMessage());  	

    String accnum = null;

    String sep = ".";

    try {

    } catch (PropertyNotFoundException pnfe) {

    	logMetacat.error("could not get property 'accNumSeparator'.  setting to '.': " 

    			+ pnfe.getMessage());  	

        }

        try {

        } catch (PropertyNotFoundException pnfe) {

        	logMetacat.error("Could not retrieve account number separator. " 

        			+ "Separator set to '.' : " + pnfe.getMessage());

    /**

	 * Writes debug information into a file. In metacat.properties, if property

	 * metacat.properties.

	 * 

	 */

	public static void writeDebugToFile(String debugInfo) {

		String debug = "false";

		try {

			if (debug != null && debug.equalsIgnoreCase("true")) {

				File outputFile = 

				FileOutputStream fos = new FileOutputStream(outputFile, true);

				PrintWriter pw = new PrintWriter(fos);

				pw.println(debugInfo);

	public static void writeDebugToDelimiteredFile(String debugInfo, boolean newLine) {

		String debug = "false";

		try {

			if (debug != null && debug.equalsIgnoreCase("true")) {

				File outputFile = new File(PropertyService

				FileOutputStream fos = new FileOutputStream(outputFile, true);

				PrintWriter pw = new PrintWriter(fos);

				if (newLine) {

    static {

    	int qryRsltCacheSize = 0;

    	try {

    	} catch (PropertyNotFoundException pnfe) {

    		System.err.println("Could not get QUERYRESULTCACHESIZE property in static block: "

					+ pnfe.getMessage());

    {

    	// since the query will be too long to be handled, so we divided the 

    	// docids vector into couple vectors.

    	logMetacat.info("The size of select doicds is "+docids.size());

    	logMetacat.info("The application result size in metacat.properties is "+size);

    	Vector subset = new Vector();

         {

           qspec = new QuerySpecification(xmlquery,

                                          parserName,

         }

         catch (Exception ee)

         {

      {

        // for html page, we put everything into one page

        offset =

      }

      else

      {

          offset =

      }

      /*

      String selectionAndExtendedQuery = null;

      // we only get cache for public

      if (user != null && user.equalsIgnoreCase("public") 

      {

    	  selectionAndExtendedQuery = query +qspec.getReturnDocList()+qspec.getReturnFieldList();

   	      String cachedResult = getResultXMLFromCache(selectionAndExtendedQuery);

           document = new StringBuffer();

           String completeDocid = docid

           completeDocid += rev;

           document.append("<docid>").append(completeDocid).append("</docid>");

           if (docname != null)

     // now we only cached none-paged query and user is public

     if (user != null && user.equalsIgnoreCase("public") 

     {

       //System.out.println("the string stored into cache is "+ resultsetBuffer.toString());

  	   storeQueryResultIntoCache(selectionAndExtendedQuery, resultsetBuffer.toString());

     int usage_count = getXmlReturnfieldsTableId(qspec, dbconn);

     boolean enterRecords = false;

     int count = (new Integer(PropertyService

                            .intValue();

     // set enterRecords to true if usage_count is more than the offset

     String element = null;

     String query = null;

     int offset = (new Integer(PropertyService

                               .intValue();

     while (keys.hasNext())

     {

                }

                String docidPlusVersion = ((String) docIdList.elementAt(i))

                //create new documentImpl object

                DocumentImpl documentImplObject = new DocumentImpl(

                version = currentVersion;

                //get package zip entry name

                //it should be docId.revsion.package

                        + "package";

                //get the whole id list for data packadge

                docIdList = getCurrentDocidListForDataPackage(packageId);

            {

                rootName = docIdString

                //get the whole id list for data packadge

                docIdList = getOldVersionDocidListForDataPackage(docIdString);

                            // Add String object to htmlDocumentImplList

                            String elementInHtmlList = remoteDoc

                                    .getDocIdWithoutRevsion()

                                    + remoteDoc.getRevision();

                            htmlDocumentImplList.add(elementInHtmlList);

                        }//if

                        writeSitemapHeader(sitemap);

                    }

                    String docid = rs.getString(1) + separator

                            + rs.getString(2);

                    writeSitemapEntry(sitemap, docid);

        try

        {

            PermissionController control = new PermissionController(docid

            //unChangableSubTreeHash = getUnchangableSubTree(control, user,

            // groups);

                String docidWithoutRev = MetaCatUtil.getDocIdFromString(docid);

                String seperator = ".";

                try {

				} catch (PropertyNotFoundException pnfe) {

					logMetacat.error("Could not get property 'accNumSeparator'.  " 

							+ "Setting separator to '.': "+ pnfe.getMessage());

        // Get the unchangable subtrees (user doesn't have write permission)

        try {

            PermissionController control = new PermissionController(docid

            //unChangableSubTreeHash = getUnchangableSubTree(control, user,

            // groups);

                String docidWithoutRev = MetaCatUtil.getDocIdFromString(docid);

                String seperator = ".";

                try {

                } catch (PropertyNotFoundException pnfe) {

                	logMetacat.error("Could not fing property 'accNumSeparator'. " 

                			+ "Setting separator to '.': " + pnfe.getMessage());

	public DocumentIdentifier(String docid) throws AccessionNumberException {

		this.docid = docid;

		try {

		} catch (PropertyNotFoundException pnfe) {

			throw new AccessionNumberException(

					"Could not get property 'accNumSeparator' :" + pnfe.getMessage());

    userName = myUserName;

    passWord = myPassWord;

    zipEntry = myZipEntryPath+ docIdWithoutRevision + 

  }// Constructor

      throw new Exception ("Couldn't find a dataset docid for the required id");

    }

    // Create a documentImpl object

    DBUtil.getLatestRevisionInDocumentTable(givenDocId);

    document = new DocumentImpl(accNumber, false);

    // get the replication home server (it come from xml_replication table)

    }

    // User specified docid (including revision number

    String specifiedDocId = docIdWithoutRevision + 

    logMetacat.info("The requried docid is: "+ specifiedDocId);

    // At first login to remote metacat server. 

    }

    // User specified docid (including revision number

    String specifiedDocId = docIdWithoutRevision + 

    logMetacat.info("The requried docid is: "+ specifiedDocId);

    // At first login to remote metacat server.

  {

		String parserName = PropertyService.getProperty("saxparser");

		this.server = SystemUtil.getSecureServerURL();

		this.connection = conn;

		this.parserName = parserName;