/src/edu/ucsb/nceas/metacat/Eml210SAXHandler.java - Annotate - Metacat - Ecoinformatics Redmine

metacat/src/edu/ucsb/nceas/metacat/Eml210SAXHandler.java @ 9237

-            sgarg
+/**
  *  '$RCSfile$'
  *    Purpose: A Class that handles the SAX XML events as they
  *             are generated from XML documents
  *  Copyright: 2000 Regents of the University of California and the
  *             National Center for Ecological Analysis and Synthesis
  *    Authors: Matt Jones, Jivka Bojilova
+ *
  *   '$Author$'
  *     '$Date$'
  * '$Revision$'
+ *
  * 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.File;
-            leinfelder
+import java.io.FileOutputStream;
-            sgarg
+import java.io.IOException;
-            leinfelder
+import java.io.OutputStreamWriter;
 import java.io.Writer;
-            sgarg
+import java.sql.PreparedStatement;
 import java.sql.ResultSet;
 import java.sql.SQLException;
-            leinfelder
+import java.util.Date;
-            sgarg
+import java.util.EmptyStackException;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.Stack;
 import java.util.Vector;
-            sgarg
+import org.apache.log4j.Logger;
-            sgarg
+import org.xml.sax.Attributes;
 import org.xml.sax.SAXException;
-            leinfelder
+import edu.ucsb.nceas.utilities.access.AccessControlInterface;
-            daigle
+import edu.ucsb.nceas.metacat.accesscontrol.AccessRule;
 import edu.ucsb.nceas.metacat.accesscontrol.AccessSection;
-            daigle
+import edu.ucsb.nceas.metacat.database.DBConnection;
 import edu.ucsb.nceas.metacat.database.DBConnectionPool;
-            leinfelder
+import edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService;
-            daigle
+import edu.ucsb.nceas.metacat.properties.PropertyService;
-            daigle
+import edu.ucsb.nceas.metacat.util.DocumentUtil;
-            daigle
+import edu.ucsb.nceas.metacat.util.MetacatUtil;
-            daigle
+import edu.ucsb.nceas.utilities.PropertyNotFoundException;
-            sgarg
+/**
-            daigle
+ * A database aware Class implementing callback methods for the SAX parser to
-            sgarg
+ * call when processing the XML stream and generating events
  */
-            daigle
+public class Eml210SAXHandler extends DBSAXHandler implements AccessControlInterface {
             sgarg
-            daigle
+	private boolean processingTopLevelAccess = false;
             sgarg
-            daigle
+	private boolean processingAdditionalAccess = false;
             sgarg
-            daigle
+	private boolean processingOtherAccess = false;
             sgarg
-            daigle
+	private AccessSection accessObject = null;
             sgarg
-            daigle
+	private AccessRule accessRule = null;
             sgarg
-            daigle
+	// all access rules
 	private Vector<AccessSection> accessObjectList = new Vector<AccessSection>();
             sgarg
-            daigle
+	private Hashtable<String, AccessSection> topLevelAccessControlMap = new Hashtable<String, AccessSection>();
             sgarg
-            daigle
+	// subtree access for additionalmetadata
 	private Hashtable<String, AccessSection> additionalAccessControlMap = new Hashtable<String, AccessSection>();
 	private Vector<Hashtable<String, AccessSection>> additionalAccessMapList = new Vector<Hashtable<String, AccessSection>>();
 	// ids from additionalmetadata/describes
 	private Vector<String> describesId = new Vector<String>();
-            daigle
+	private Stack<SubTree> subTreeInfoStack = new Stack<SubTree>();
             sgarg
-            daigle
+	private Vector<SubTree> subTreeList = new Vector<SubTree>();
             daigle
 	private boolean needToCheckAccessModule = false;
             sgarg
-            daigle
+	private Vector<AccessSection> unChangeableAccessSubTreeVector = new Vector<AccessSection>();
             sgarg
-            daigle
+	private Stack<NodeRecord> currentUnchangeableAccessModuleNodeStack = new Stack<NodeRecord>();
             sgarg
-            daigle
+	private AccessSection topAccessSection;
             sgarg
-            daigle
+	// we need an another stack to store the access node which we pull out just
 	// from xml. If a reference happened, we can use the stack the compare nodes
 	private Stack<NodeRecord> storedAccessNodeStack = new Stack<NodeRecord>();
             sgarg
-            daigle
+	// vector stored the data file id which will be write into relation table
 	private Vector<String> onlineDataFileIdInRelationVector = new Vector<String>();
             sgarg
-            daigle
+	// vector stored the data file id which will be write top access rules to
 	// access table
 	private Vector<String> onlineDataFileIdInTopAccessVector = new Vector<String>();
             sgarg
-            daigle
+	// Indicator of inline data
 	private boolean handleInlineData = false;
             sgarg
-            daigle
+	private Hashtable<String, String> inlineDataNameSpace = null;
             sgarg
-            leinfelder
+	private Writer inlineDataFileWriter = null;
             sgarg
-            daigle
+	private String inlineDataFileName = null;
             sgarg
-            daigle
+	DistributionSection currentDistributionSection = null;
             sgarg
-            daigle
+	Vector<DistributionSection> allDistributionSections = new Vector<DistributionSection>();
-            slaughter
+    private Vector<String> guidsToSync;
             daigle
 	// This variable keeps a counter of each distribution element. This index
 	// will be used to name the inline data file that gets written to disk, and to
 	// strip inline data from the metadata document on file if the user does not have
 	// read access.
-            daigle
+	private int distributionIndex = 0;
             sgarg
-            daigle
+	// private String distributionOnlineFileName = null;
-            daigle
+	// This is used to delete inline files if the xml does not parse correctly.
-            daigle
+	private Vector<String> inlineFileIdList = new Vector<String>();
             sgarg
-            daigle
+	// Constant
 	private static final String EML = "eml";
             sgarg
-            daigle
+	private static final String DISTRIBUTION = "distribution";
             sgarg
-            daigle
+	private static final String ORDER = "order";
             sgarg
-            daigle
+	private static final String ID = "id";
             sgarg
-            daigle
+	private static final String REFERENCES = "references";
             sgarg
-            daigle
+	public static final String INLINE = "inline";
             sgarg
-            daigle
+	private static final String ONLINE = "online";
             sgarg
-            daigle
+	private static final String URL = "url";
             sgarg
-            daigle
+	// private static final String PERMISSIONERROR = "User tried to update a
 	// subtree "
 	// + "when they don't have write permission!";
             sgarg
-            daigle
+	private static final String UPDATEACCESSERROR = "User tried to update an "
 			+ "access module when they don't have \"ALL\" permission!";
             sgarg
-            daigle
+	private static final String TOPLEVEL = "top";
             sgarg
-            daigle
+	private static final String SUBTREELEVEL = "subtree";
             sgarg
-            daigle
+	private static final String RELATION = "Provides info for";
             sgarg
-            daigle
+	private Logger logMetacat = Logger.getLogger(Eml210SAXHandler.class);
             sgarg
-            daigle
+	/**
 	 * Construct an instance of the handler class In this constructor, user can
 	 * specify the version need to update
+	 *
 	 * @param conn
 	 *            the JDBC connection to which information is written
 	 * @param action -
 	 *            "INSERT" or "UPDATE"
 	 * @param docid
 	 *            to be inserted or updated into JDBC connection
 	 * @param revision,
 	 *            the user specified the revision need to be update
 	 * @param user
 	 *            the user connected to MetaCat servlet and owns the document
 	 * @param groups
 	 *            the groups to which user belongs
 	 * @param pub
 	 *            flag for public "read" access on document
 	 * @param serverCode
 	 *            the serverid from xml_replication on which this document
 	 *            resides.
+	 *
 	 */
 	public Eml210SAXHandler(DBConnection conn, String action, String docid,
 			String revision, String user, String[] groups, String pub, int serverCode,
-            slaughter
+			Date createDate, Date updateDate, boolean writeAccessRules, Vector<String> guidsToSync) throws SAXException {
-            daigle
+		super(conn, action, docid, revision, user, groups, pub, serverCode, createDate,
-            leinfelder
+				updateDate, writeAccessRules);
             slaughter
 		this.guidsToSync = guidsToSync;
-            daigle
+		// Get the unchangeable subtrees (user doesn't have write permission)
 		try {
             sgarg
-            leinfelder
+			if (action.equals("UPDATE")) {
 				// If the action is update and user doesn't have "ALL" permission
 				// we need to check if user can update access subtree
 				int latestRevision = DBUtil.getLatestRevisionInDocumentTable(docid);
 				String previousDocid =
 					docid + PropertyService.getProperty("document.accNumSeparator") + latestRevision;
 				PermissionController control = new PermissionController(previousDocid );
 				if (!control.hasPermission(user, groups, AccessControlInterface.ALLSTRING)
 						&& action != null) {
 					needToCheckAccessModule = true;
 					unChangeableAccessSubTreeVector = getAccessSubTreeListFromDB();
+				}
             daigle
 		} catch (Exception e) {
 			throw new SAXException(e.getMessage());
+		}
+	}
 	/*
 	 * Get the subtree node info from xml_accesssubtree table
 	 */
 	private Vector<AccessSection> getAccessSubTreeListFromDB() throws Exception {
 		Vector<AccessSection> result = new Vector<AccessSection>();
 		PreparedStatement pstmt = null;
 		ResultSet rs = null;
 		String sql = "SELECT controllevel, subtreeid, startnodeid, endnodeid "
 				+ "FROM xml_accesssubtree WHERE docid like ? "
 				+ "ORDER BY startnodeid ASC";
             sgarg
-            daigle
+		try {
             sgarg
-            daigle
+			pstmt = connection.prepareStatement(sql);
 			// Increase DBConnection usage count
 			connection.increaseUsageCount(1);
 			// Bind the values to the query
 			pstmt.setString(1, docid);
 			pstmt.execute();
             sgarg
-            daigle
+			// Get result set
 			rs = pstmt.getResultSet();
 			while (rs.next()) {
 				String level = rs.getString(1);
 				String sectionId = rs.getString(2);
 				long startNodeId = rs.getLong(3);
 				long endNodeId = rs.getLong(4);
 				// create a new access section
 				AccessSection accessObj = new AccessSection();
 				accessObj.setControlLevel(level);
 				accessObj.setDocId(docid);
 				accessObj.setSubTreeId(sectionId);
 				accessObj.setStartNodeId(startNodeId);
 				accessObj.setEndNodeId(endNodeId);
 				Stack<NodeRecord> nodeStack = accessObj.getSubTreeNodeStack();
 				accessObj.setSubTreeNodeStack(nodeStack);
 				// add this access obj into vector
 				result.add(accessObj);
 				// Get the top level access subtree control
 				if (level != null && level.equals(TOPLEVEL)) {
 					topAccessSection = accessObj;
+				}
+			}
 			pstmt.close();
 		}// try
 		catch (SQLException e) {
 			throw new SAXException("EMLSAXHandler.getAccessSubTreeListFromDB(): "
 					+ e.getMessage());
 		}// catch
 		finally {
 			try {
 				pstmt.close();
 			} catch (SQLException ee) {
 				throw new SAXException("EMLSAXHandler.getAccessSubTreeListFromDB(): "
 						+ ee.getMessage());
+			}
 		}// finally
 		return result;
+	}
             sgarg
-            daigle
+	/** SAX Handler that is called at the start of each XML element */
 	public void startElement(String uri, String localName, String qName, Attributes atts)
 			throws SAXException {
 		// for element <eml:eml...> qname is "eml:eml", local name is "eml"
 		// for element <acl....> both qname and local name is "eml"
 		// uri is namesapce
 		logMetacat.debug("Start ELEMENT(qName) " + qName);
 		logMetacat.debug("Start ELEMENT(localName) " + localName);
 		logMetacat.debug("Start ELEMENT(uri) " + uri);
             sgarg
-            daigle
+		DBSAXNode parentNode = null;
 		DBSAXNode currentNode = null;
             sgarg
-            daigle
+		if (!handleInlineData) {
 			// Get a reference to the parent node for the id
 			try {
 				parentNode = (DBSAXNode) nodeStack.peek();
 			} catch (EmptyStackException e) {
 				parentNode = null;
+			}
             sgarg
-            daigle
+			// start handle inline data
 			if (localName.equals(INLINE)) {
 				handleInlineData = true;
 				// initialize namespace hash for in line data
 				inlineDataNameSpace = new Hashtable<String, String>();
 				// initialize file writer
-            daigle
+				String docidWithoutRev = DocumentUtil.getDocIdFromString(docid);
-            daigle
+				String seperator = ".";
 				try {
 					seperator = PropertyService.getProperty("document.accNumSeparator");
 				} catch (PropertyNotFoundException pnfe) {
 					logMetacat.error("Could not fing property 'accNumSeparator'. "
 							+ "Setting separator to '.': " + pnfe.getMessage());
+				}
 				// the new file name will look like docid.rev.2
 				inlineDataFileName = docidWithoutRev + seperator + revision + seperator
-            daigle
+						+ distributionIndex;
-            leinfelder
+				inlineDataFileWriter = createInlineDataFileWriter(inlineDataFileName, encoding);
-            daigle
+				// put the inline file id into a vector. If upload failed,
 				// metacat will delete the inline data file
 				inlineFileIdList.add(inlineDataFileName);
 				currentDistributionSection.setDistributionType(DistributionSection.INLINE_DATA_DISTRIBUTION);
 				currentDistributionSection.setDataFileName(inlineDataFileName);
             sgarg
             daigle
             sgarg
-            daigle
+			// If hit a text node, we need write this text for current's parent
 			// node This will happen if the element is mixed
 			if (hitTextNode && parentNode != null) {
             sgarg
-            daigle
+				// compare top level access module
-            daigle
+				if (processingTopLevelAccess && needToCheckAccessModule) {
 					compareAccessTextNode(currentUnchangeableAccessModuleNodeStack, textBuffer);
             daigle
             sgarg
-            daigle
+				if (needToCheckAccessModule
-            daigle
+						&& (processingAdditionalAccess || processingOtherAccess || processingTopLevelAccess)) {
-            daigle
+					// stored the pull out nodes into storedNode stack
 					NodeRecord nodeElement = new NodeRecord(-2, -2, -2, "TEXT", null,
-            daigle
+							null, MetacatUtil.normalize(textBuffer.toString()));
-            daigle
+					storedAccessNodeStack.push(nodeElement);
             sgarg
             daigle
             sgarg
-            daigle
+				// write the textbuffer into db for parent node.
 				endNodeId = writeTextForDBSAXNode(endNodeId, textBuffer, parentNode);
 				// rest hitTextNode
 				hitTextNode = false;
 				// reset textbuffer
 				textBuffer = null;
 				textBuffer = new StringBuffer();
             sgarg
             daigle
             sgarg
-            daigle
+			// Document representation that points to the root document node
 			if (atFirstElement) {
 				atFirstElement = false;
 				// If no DOCTYPE declaration: docname = root element
 				// doctype = root element name or name space
 				if (docname == null) {
 					docname = localName;
 					// if uri isn't null doctype = uri(namespace)
 					// othewise root element
 					if (uri != null && !(uri.trim()).equals("")) {
 						doctype = uri;
 					} else {
 						doctype = docname;
+					}
 					logMetacat.debug("DOCNAME-a: " + docname);
 					logMetacat.debug("DOCTYPE-a: " + doctype);
 				} else if (doctype == null) {
 					// because docname is not null and it is declared in dtd
 					// so could not be in schema, no namespace
 					doctype = docname;
 					logMetacat.debug("DOCTYPE-b: " + doctype);
+				}
 				rootNode.writeNodename(docname);
 				try {
 					// for validated XML Documents store a reference to XML DB
 					// Catalog. Because this is select statement and it needn't
 					// roll back if insert document action failed. In order to
 					// decrease DBConnection usage count, we get a new
 					// dbconnection from pool String catalogid = null;
 					DBConnection dbConn = null;
 					int serialNumber = -1;
             sgarg
-            daigle
+					try {
 						// Get dbconnection
 						dbConn = DBConnectionPool
 								.getDBConnection("DBSAXHandler.startElement");
 						serialNumber = dbConn.getCheckOutSerialNumber();
             leinfelder
 						String sql = "SELECT catalog_id FROM xml_catalog "
 							+ "WHERE entry_type = 'Schema' "
 							+ "AND public_id = ?";
 						PreparedStatement pstmt = dbConn.prepareStatement(sql);
 						pstmt.setString(1, doctype);
 						ResultSet rs = pstmt.executeQuery();
-            daigle
+						boolean hasRow = rs.next();
 						if (hasRow) {
 							catalogid = rs.getString(1);
+						}
-            leinfelder
+						pstmt.close();
-            daigle
+					}// try
 					finally {
 						// Return dbconnection
 						DBConnectionPool.returnDBConnection(dbConn, serialNumber);
 					}// finally
             sgarg
-            daigle
+					// create documentImpl object by the constructor which can
 					// specify the revision
 					if (!super.getIsRevisionDoc()) {
 						currentDocument = new DocumentImpl(connection, rootNode
 								.getNodeID(), docname, doctype, docid, revision, action,
 								user, this.pub, catalogid, this.serverCode, createDate,
 								updateDate);
+					}
             sgarg
-            daigle
+				} catch (McdbDocNotFoundException mdnfe) {
 					Vector<Integer> revList = null;
 					try {
 						revList = DBUtil.getRevListFromRevisionTable(docid);
 					} catch (SQLException sqle) {
 						logMetacat.error("SQL error when trying to get rev list for doc " + docid + " : " + sqle.getMessage());
 						throw (new SAXException("Doc ID " + docid + " was not found and cannot be updated."));
+					}
 					if (revList.size() > 0) {
-            daigle
+						throw (new SAXException("EML210SaxHandler.startElement - Doc ID " + docid + " was deleted and cannot be updated."));
-            daigle
+					} else {
-            daigle
+						throw (new SAXException("EML210SaxHandler.startElement - Doc ID " + docid + " was not found and cannot be updated."));
             daigle
 				} catch (Exception e) {
-            daigle
+                    throw (new SAXException("EML210SaxHandler.startElement - error with action " +
                     		action + " : " + e.getMessage()));
             daigle
+			}
             sgarg
-            daigle
+			// Create the current node representation
 			currentNode = new DBSAXNode(connection, qName, localName, parentNode,
 					rootNode.getNodeID(), docid, doctype);
 			// Use a local variable to store the element node id
 			// If this element is a start point of subtree(section), it will be
 			// stored otherwise, it will be discarded
 			long startNodeId = currentNode.getNodeID();
 			// Add all of the namespaces
 			String prefix = null;
 			String nsuri = null;
 			Enumeration<String> prefixes = namespaces.keys();
 			while (prefixes.hasMoreElements()) {
 				prefix = prefixes.nextElement();
 				nsuri = namespaces.get(prefix);
 				endNodeId = currentNode.setNamespace(prefix, nsuri, docid);
+			}
             sgarg
-            daigle
+			// Add all of the attributes
 			for (int i = 0; i < atts.getLength(); i++) {
 				String attributeName = atts.getQName(i);
 				String attributeValue = atts.getValue(i);
 				endNodeId = currentNode
 						.setAttribute(attributeName, attributeValue, docid);
             sgarg
-            daigle
+				// To handle name space and schema location if the attribute
 				// name is xsi:schemaLocation. If the name space is in not
 				// in catalog table it will be registered.
 				if (attributeName != null
 						&& attributeName.indexOf(MetaCatServlet.SCHEMALOCATIONKEYWORD) != -1) {
 					SchemaLocationResolver resolver = new SchemaLocationResolver(
 							attributeValue);
 					resolver.resolveNameSpace();
             sgarg
-            daigle
+				} else if (attributeName != null && attributeName.equals(ID)) {
             daigle
             daigle
 			}// for
 			// handle access stuff
 			if (localName.equals(ACCESS)) {
 				if (parentNode.getTagName().equals(EML)) {
-            daigle
+					processingTopLevelAccess = true;
-            daigle
+				} else if (parentNode.getTagName() == DISTRIBUTION) {
-            daigle
+					processingAdditionalAccess = true;
-            daigle
+				} else {
 					// process other access embedded into resource level
 					// module
-            daigle
+					processingOtherAccess = true;
             daigle
-            daigle
+				// create access object
 				accessObject = new AccessSection();
 				// set permission order
 				String permOrder = currentNode.getAttribute(ORDER);
 				accessObject.setPermissionOrder(permOrder);
 				// set access id
 				String accessId = currentNode.getAttribute(ID);
 				accessObject.setSubTreeId(accessId);
 				accessObject.setStartNodeId(startNodeId);
 				accessObject.setDocId(docid);
-            daigle
+				if (processingAdditionalAccess) {
-            daigle
+					accessObject.setDataFileName(inlineDataFileName);
+				}
             sgarg
-            daigle
+				// load top level node stack to
 				// currentUnchangableAccessModuleNodeStack
-            daigle
+				if (processingTopLevelAccess && needToCheckAccessModule) {
-            daigle
+					// get the node stack for
 					currentUnchangeableAccessModuleNodeStack = topAccessSection
 							.getSubTreeNodeStack();
+				}
 			} else if (localName.equals(DISTRIBUTION)) {
 				distributionIndex++;
 				currentDistributionSection = new DistributionSection(distributionIndex);
             sgarg
-            daigle
+				// handle subtree info
 				SubTree subTree = new SubTree();
 				// set sub tree id
 				subTree.setSubTreeId(String.valueOf(distributionIndex));
 				// set sub tree start element name
 				subTree.setStartElementName(currentNode.getTagName());
 				// set start node number
 				subTree.setStartNodeId(startNodeId);
 				// add to stack, but it didn't get end node id yet
 				subTreeInfoStack.push(subTree);
+			}
 			// Set up a access rule for allow
 			else if (parentNode.getTagName() != null
 					&& (parentNode.getTagName()).equals(ACCESS)
 					&& localName.equals(ALLOW)) {
             sgarg
-            daigle
+				accessRule = new AccessRule();
             sgarg
-            daigle
+				// set permission type "allow"
 				accessRule.setPermissionType(ALLOW);
             sgarg
             daigle
 			// set up an access rule for deny
 			else if (parentNode.getTagName() != null
 					&& (parentNode.getTagName()).equals(ACCESS) && localName.equals(DENY)) {
 				accessRule = new AccessRule();
 				// set permission type "allow"
 				accessRule.setPermissionType(DENY);
+			}
             sgarg
-            daigle
+			// Add the node to the stack, so that any text data can be
 			// added as it is encountered
 			nodeStack.push(currentNode);
 			// Add the node to the vector used by thread for writing XML Index
 			nodeIndex.addElement(currentNode);
             sgarg
-            daigle
+			// compare top access level module
-            daigle
+			if (processingTopLevelAccess && needToCheckAccessModule) {
-            daigle
+				compareElementNameSpaceAttributes(
 						currentUnchangeableAccessModuleNodeStack, namespaces, atts,
 						localName, UPDATEACCESSERROR);
             sgarg
             daigle
             sgarg
-            daigle
+			// store access module element and attributes into stored stack
 			if (needToCheckAccessModule
-            daigle
+					&& (processingAdditionalAccess || processingOtherAccess || processingTopLevelAccess)) {
-            daigle
+				// stored the pull out nodes into storedNode stack
 				NodeRecord nodeElement = new NodeRecord(-2, -2, -2, "ELEMENT", localName,
-            daigle
+						prefix, MetacatUtil.normalize(null));
-            daigle
+				storedAccessNodeStack.push(nodeElement);
 				for (int i = 0; i < atts.getLength(); i++) {
 					String attributeName = atts.getQName(i);
 					String attributeValue = atts.getValue(i);
 					NodeRecord nodeAttribute = new NodeRecord(-2, -2, -2, "ATTRIBUTE",
-            daigle
+							attributeName, null, MetacatUtil.normalize(attributeValue));
-            daigle
+					storedAccessNodeStack.push(nodeAttribute);
+				}
             sgarg
             daigle
             sgarg
-            daigle
+			// reset name space
 			namespaces = null;
 			namespaces = new Hashtable<String, String>();
 		}// not inline data
 		else {
 			// we don't buffer the inline data in characters() method
 			// so start character don't need to hand text node.
             sgarg
-            daigle
+			// inline data may be the xml format.
 			StringBuffer inlineElements = new StringBuffer();
 			inlineElements.append("<").append(qName);
 			// append attributes
 			for (int i = 0; i < atts.getLength(); i++) {
 				String attributeName = atts.getQName(i);
 				String attributeValue = atts.getValue(i);
 				inlineElements.append(" ");
 				inlineElements.append(attributeName);
 				inlineElements.append("=\"");
 				inlineElements.append(attributeValue);
 				inlineElements.append("\"");
+			}
 			// append namespace
 			String prefix = null;
 			String nsuri = null;
 			Enumeration<String> prefixes = inlineDataNameSpace.keys();
 			while (prefixes.hasMoreElements()) {
 				prefix = prefixes.nextElement();
 				nsuri = namespaces.get(prefix);
 				inlineElements.append(" ");
 				inlineElements.append("xmlns:");
 				inlineElements.append(prefix);
 				inlineElements.append("=\"");
 				inlineElements.append(nsuri);
 				inlineElements.append("\"");
+			}
 			inlineElements.append(">");
 			// reset inline data name space
 			inlineDataNameSpace = null;
 			inlineDataNameSpace = new Hashtable<String, String>();
 			// write inline data into file
 			logMetacat.debug("the inline element data is: " + inlineElements.toString());
 			writeInlineDataIntoFile(inlineDataFileWriter, inlineElements);
 		}// else
             sgarg
             daigle
             sgarg
-            daigle
+	private void compareElementNameSpaceAttributes(
 			Stack<NodeRecord> unchangeableNodeStack,
 			Hashtable<String, String> nameSpaces, Attributes attributes,
 			String localName, String error) throws SAXException {
 		// Get element subtree node stack (element node)
 		NodeRecord elementNode = null;
 		try {
 			elementNode = unchangeableNodeStack.pop();
 		} catch (EmptyStackException ee) {
 			logMetacat.error("Node stack is empty for element data");
 			throw new SAXException(error);
+		}
 		logMetacat.debug("current node type from xml is ELEMENT");
 		logMetacat.debug("node type from stack: " + elementNode.getNodeType());
 		logMetacat.debug("node name from xml document: " + localName);
 		logMetacat.debug("node name from stack: " + elementNode.getNodeName());
 		logMetacat.debug("node data from stack: " + elementNode.getNodeData());
 		logMetacat.debug("node id is: " + elementNode.getNodeId());
 		// if this node is not element or local name not equal or name space
 		// not equals, throw an exception
 		if (!elementNode.getNodeType().equals("ELEMENT")
 				|| !localName.equals(elementNode.getNodeName()))
 		// (uri != null && !uri.equals(elementNode.getNodePrefix())))
+		{
 			logMetacat.error("Inconsistence happened: ");
 			logMetacat.error("current node type from xml is ELEMENT");
 			logMetacat.error("node type from stack: " + elementNode.getNodeType());
 			logMetacat.error("node name from xml document: " + localName);
 			logMetacat.error("node name from stack: " + elementNode.getNodeName());
 			logMetacat.error("node data from stack: " + elementNode.getNodeData());
 			logMetacat.error("node id is: " + elementNode.getNodeId());
 			throw new SAXException(error);
+		}
             sgarg
-            daigle
+		// compare namespace
 		Enumeration<String> nameEn = nameSpaces.keys();
 		while (nameEn.hasMoreElements()) {
 			// Get namespacke node stack (element node)
 			NodeRecord nameNode = null;
 			try {
 				nameNode = unchangeableNodeStack.pop();
 			} catch (EmptyStackException ee) {
 				logMetacat.error("Node stack is empty for namespace data");
 				throw new SAXException(error);
+			}
             sgarg
-            daigle
+			String prefixName = nameEn.nextElement();
 			String nameSpaceUri = nameSpaces.get(prefixName);
 			if (!nameNode.getNodeType().equals("NAMESPACE")
 					|| !prefixName.equals(nameNode.getNodeName())
 					|| !nameSpaceUri.equals(nameNode.getNodeData())) {
 				logMetacat.error("Inconsistence happened: ");
 				logMetacat.error("current node type from xml is NAMESPACE");
 				logMetacat.error("node type from stack: " + nameNode.getNodeType());
 				logMetacat.error("current node name from xml is: " + prefixName);
 				logMetacat.error("node name from stack: " + nameNode.getNodeName());
 				logMetacat.error("current node data from xml is: " + nameSpaceUri);
 				logMetacat.error("node data from stack: " + nameNode.getNodeData());
 				logMetacat.error("node id is: " + nameNode.getNodeId());
 				throw new SAXException(error);
+			}
             sgarg
-            daigle
+		}// while
             sgarg
-            daigle
+		// compare attributes
 		for (int i = 0; i < attributes.getLength(); i++) {
 			NodeRecord attriNode = null;
 			try {
 				attriNode = unchangeableNodeStack.pop();
             sgarg
-            daigle
+			} catch (EmptyStackException ee) {
 				logMetacat.error("Node stack is empty for attribute data");
 				throw new SAXException(error);
+			}
 			String attributeName = attributes.getQName(i);
 			String attributeValue = attributes.getValue(i);
 			logMetacat.debug("current node type from xml is ATTRIBUTE ");
 			logMetacat.debug("node type from stack: " + attriNode.getNodeType());
 			logMetacat.debug("current node name from xml is: " + attributeName);
 			logMetacat.debug("node name from stack: " + attriNode.getNodeName());
 			logMetacat.debug("current node data from xml is: " + attributeValue);
 			logMetacat.debug("node data from stack: " + attriNode.getNodeData());
 			logMetacat.debug("node id  is: " + attriNode.getNodeId());
             sgarg
-            daigle
+			if (!attriNode.getNodeType().equals("ATTRIBUTE")
 					|| !attributeName.equals(attriNode.getNodeName())
 					|| !attributeValue.equals(attriNode.getNodeData())) {
 				logMetacat.error("Inconsistence happened: ");
 				logMetacat.error("current node type from xml is ATTRIBUTE ");
 				logMetacat.error("node type from stack: " + attriNode.getNodeType());
 				logMetacat.error("current node name from xml is: " + attributeName);
 				logMetacat.error("node name from stack: " + attriNode.getNodeName());
 				logMetacat.error("current node data from xml is: " + attributeValue);
 				logMetacat.error("node data from stack: " + attriNode.getNodeData());
 				logMetacat.error("node is: " + attriNode.getNodeId());
 				throw new SAXException(error);
+			}
 		}// for
             sgarg
             daigle
             sgarg
-            daigle
+	/* method to compare current text node and node in db */
-            daigle
+	private void compareAccessTextNode(Stack<NodeRecord> nodeStack, StringBuffer text) throws SAXException {
-            daigle
+		NodeRecord node = null;
 		// get node from current stack
 		try {
 			node = nodeStack.pop();
 		} catch (EmptyStackException ee) {
-            daigle
+			logMetacat.error("Node stack is empty for text data in startElement for doc id " + docid);
 			throw new SAXException("Access rules could not be found in database.");
             daigle
             daigle
 		String dbAccessData = node.getNodeData();
 		String docAccessData = text.toString().trim();
 		logMetacat.debug("Eml210SAXHandler.compareAccessTextNode - \n" +
 					"\t access node type from db:       " + node.getNodeType() + "\n" +
 					"\t access node data from db:       " + node.getNodeData() + "\n" +
 					"\t access node data from document: " + text.toString());
-            daigle
+		if (!node.getNodeType().equals("TEXT")
-            daigle
+				|| !docAccessData.equals(dbAccessData)) {
 			logMetacat.warn("Eml210SAXHandler.compareAccessTextNode - Access record mismatch: \n" +
 					"\t access node type from db:       " + node.getNodeType() + "\n" +
 					"\t access node data from db:       " + dbAccessData + "\n" +
 					"\t access node data from document: " + docAccessData);
 			throw new SAXException(UPDATEACCESSERROR + " [Eml210SAXHandler.compareAccessTextNode]");
-            daigle
+		}// if
+	}
             sgarg
-            daigle
+	/** SAX Handler that is called for each XML text node */
 	public void characters(char[] cbuf, int start, int len) throws SAXException {
 		logMetacat.debug("CHARACTERS");
 		if (!handleInlineData) {
 			// buffer all text nodes for same element. This is for if text was
 			// split into different nodes
 			textBuffer.append(new String(cbuf, start, len));
 			// set hittextnode true
 			hitTextNode = true;
 			// if text buffer .size is greater than max, write it to db.
 			// so we can save memory
 			if (textBuffer.length() > MAXDATACHARS) {
 				logMetacat.debug("Write text into DB in charaters"
 						+ " when text buffer size is greater than maxmum number");
 				DBSAXNode currentNode = (DBSAXNode) nodeStack.peek();
 				endNodeId = writeTextForDBSAXNode(endNodeId, textBuffer, currentNode);
 				textBuffer = null;
 				textBuffer = new StringBuffer();
+			}
 		} else {
 			// this is inline data and write file system directly
 			// we don't need to buffer it.
 			StringBuffer inlineText = new StringBuffer();
 			inlineText.append(new String(cbuf, start, len));
 			logMetacat.debug("The inline text data write into file system: "
 					+ inlineText.toString());
 			writeInlineDataIntoFile(inlineDataFileWriter, inlineText);
+		}
+	}
             sgarg
-            daigle
+	/** SAX Handler that is called at the end of each XML element */
 	public void endElement(String uri, String localName, String qName)
 			throws SAXException {
 		logMetacat.debug("End ELEMENT " + qName);
             sgarg
-            daigle
+		if (localName.equals(INLINE) && handleInlineData) {
 			// Get the node from the stack
 			DBSAXNode currentNode = (DBSAXNode) nodeStack.pop();
 			logMetacat.debug("End of inline data");
 			// close file writer
 			try {
 				inlineDataFileWriter.close();
 				handleInlineData = false;
 			} catch (IOException ioe) {
 				throw new SAXException(ioe.getMessage());
+			}
             sgarg
-            daigle
+			// write put inline data file name into text buffer (without path)
 			textBuffer = new StringBuffer(inlineDataFileName);
 			// write file name into db
 			endNodeId = writeTextForDBSAXNode(endNodeId, textBuffer, currentNode);
 			// reset textbuff
 			textBuffer = null;
 			textBuffer = new StringBuffer();
 			return;
+		}
             sgarg
-            daigle
+		if (!handleInlineData) {
 			// Get the node from the stack
 			DBSAXNode currentNode = (DBSAXNode) nodeStack.pop();
 			String currentTag = currentNode.getTagName();
             sgarg
-            daigle
+			// If before the end element, the parser hit text nodes and store
 			// them into the buffer, write the buffer to data base. The reason
 			// we put write database here is for xerces some time split text
 			// node
 			if (hitTextNode) {
 				// get access value
 				String data = null;
 				// add principal
 				if (currentTag.equals(PRINCIPAL) && accessRule != null) {
 					data = (textBuffer.toString()).trim();
 					accessRule.addPrincipal(data);
             sgarg
-            daigle
+				} else if (currentTag.equals(PERMISSION) && accessRule != null) {
 					data = (textBuffer.toString()).trim();
 					// we combine different a permission into one value
 					int permission = accessRule.getPermission();
 					// add permission
 					if (data.toUpperCase().equals(READSTRING)) {
 						permission = permission | READ;
 					} else if (data.toUpperCase().equals(WRITESTRING)) {
 						permission = permission | WRITE;
 					} else if (data.toUpperCase().equals(CHMODSTRING)) {
 						permission = permission | CHMOD;
 					} else if (data.toUpperCase().equals(ALLSTRING)) {
 						permission = permission | ALL;
+					}
 					accessRule.setPermission(permission);
 				} else if (currentTag.equals(REFERENCES)
-            daigle
+						&& (processingTopLevelAccess || processingAdditionalAccess || processingOtherAccess)) {
-            daigle
+					// get reference
 					data = (textBuffer.toString()).trim();
 					// put reference id into accessSection
 					accessObject.setReferences(data);
             sgarg
-            daigle
+				} else if (currentTag.equals(URL)) {
 					// handle online data, make sure its'parent is online
 					DBSAXNode parentNode = (DBSAXNode) nodeStack.peek();
 					if (parentNode != null && parentNode.getTagName() != null
 							&& parentNode.getTagName().equals(ONLINE)) {
 						// if online data is in local metacat, add it to the
 						// vector
 						data = (textBuffer.toString()).trim();
 						handleOnlineUrlDataFile(data);
             daigle
-            daigle
+					}// if
 				}// else if
             daigle
-            daigle
+				// write text to db if it is not inline data
-            daigle
+				logMetacat.debug("Write text into DB in End Element");
             sgarg
-            daigle
+				// compare top level access module
 				if (processingTopLevelAccess && needToCheckAccessModule) {
 					compareAccessTextNode(currentUnchangeableAccessModuleNodeStack,
 							textBuffer);
             daigle
-            daigle
+				// write text node into db
 				endNodeId = writeTextForDBSAXNode(endNodeId, textBuffer, currentNode);
+			}
 			if (needToCheckAccessModule
 					&& (processingAdditionalAccess || processingOtherAccess || processingTopLevelAccess)) {
 				// stored the pull out nodes into storedNode stack
 				NodeRecord nodeElement = new NodeRecord(-2, -2, -2, "TEXT", null,
 						null, MetacatUtil.normalize(textBuffer.toString()));
 				storedAccessNodeStack.push(nodeElement);
             sgarg
             daigle
             sgarg
-            daigle
+			// set hitText false
 			hitTextNode = false;
 			// reset textbuff
 			textBuffer = null;
 			textBuffer = new StringBuffer();
             sgarg
-            daigle
+			// hand sub stree stuff
 			if (!subTreeInfoStack.empty()) {
 				SubTree tree = subTreeInfoStack.peek();// get last
 				// subtree
 				if (tree != null && tree.getStartElementName() != null
 						&& (tree.getStartElementName()).equals(currentTag)) {
 					// find the end of sub tree and set the end node id
 					tree.setEndNodeId(endNodeId);
 					// add the subtree into the final store palace
 					subTreeList.add(tree);
 					// get rid of it from stack
 					subTreeInfoStack.pop();
 				}// if
 			}// if
             sgarg
-            daigle
+			// access stuff
 			if (currentTag.equals(ALLOW) || currentTag.equals(DENY)) {
 				// finish parser access rule and assign it to new one
 				AccessRule newRule = accessRule;
 				// add the new rule to access section object
 				accessObject.addAccessRule(newRule);
 				// reset access rule
 				accessRule = null;
 			} else if (currentTag.equals(ACCESS)) {
 				// finish parsing an access section and assign it to new one
 				DBSAXNode parentNode = (DBSAXNode) nodeStack.peek();
             sgarg
-            daigle
+				accessObject.setEndNodeId(endNodeId);
             sgarg
-            daigle
+				if (parentNode != null && parentNode.getTagName() != null
 						&& parentNode.getTagName().equals(DISTRIBUTION)) {
 					describesId.add(String.valueOf(distributionIndex));
 					currentDistributionSection.setAccessSection(accessObject);
+				}
             sgarg
-            daigle
+				AccessSection newAccessObject = accessObject;
             sgarg
-            daigle
+				if (newAccessObject != null) {
             sgarg
-            daigle
+					// add the accessSection into a vector to store it
 					// if it is not a reference, need to store it
 					if (newAccessObject.getReferences() == null) {
             sgarg
-            daigle
+						newAccessObject.setStoredTmpNodeStack(storedAccessNodeStack);
 						accessObjectList.add(newAccessObject);
+					}
-            daigle
+					if (processingTopLevelAccess) {
             sgarg
-            daigle
+						// top level access control will handle whole document
 						// -docid
 						topLevelAccessControlMap.put(docid, newAccessObject);
 						// reset processtopleveraccess tag
             sgarg
-            daigle
+					}// if
-            daigle
+					else if (processingAdditionalAccess) {
-            daigle
+						// for additional control put everything in describes
 						// value
 						// and access object into hash
 						for (int i = 0; i < describesId.size(); i++) {
             sgarg
-            daigle
+							String subId = describesId.elementAt(i);
 							if (subId != null) {
 								additionalAccessControlMap.put(subId, newAccessObject);
 							}// if
 						}// for
 						// add this hashtable in to vector
             sgarg
-            daigle
+						additionalAccessMapList.add(additionalAccessControlMap);
 						// reset this hashtable in order to store another
 						// additional
 						// accesscontrol
 						additionalAccessControlMap = null;
 						additionalAccessControlMap = new Hashtable<String, AccessSection>();
 					}// if
             sgarg
-            daigle
+				}// if
 				// check if access node stack is empty after parsing top access
 				// module
             sgarg
-            daigle
+				if (needToCheckAccessModule && processingTopLevelAccess
-            daigle
+						&& !currentUnchangeableAccessModuleNodeStack.isEmpty()) {
             sgarg
-            daigle
+					logMetacat.error("Access node stack is not empty after "
 							+ "parsing access subtree");
 					throw new SAXException(UPDATEACCESSERROR);
             sgarg
             daigle
 				// reset access section object
             sgarg
-            daigle
+				accessObject = null;
             sgarg
-            daigle
+				// reset tmp stored node stack
 				storedAccessNodeStack = null;
 				storedAccessNodeStack = new Stack<NodeRecord>();
             sgarg
-            daigle
+				// reset flag
-            daigle
+				processingAdditionalAccess = false;
 				processingTopLevelAccess = false;
 				processingOtherAccess = false;
             sgarg
-            daigle
+			} else if (currentTag.equals(DISTRIBUTION)) {
 				// If the current Distribution is inline or data and it doesn't have an access section
 				// we use the top level access section (if it exists)
 				if ((currentDistributionSection.getDistributionType() == DistributionSection.DATA_DISTRIBUTION
 						|| currentDistributionSection.getDistributionType() == DistributionSection.INLINE_DATA_DISTRIBUTION)
 						&& currentDistributionSection.getAccessSection() == null
 						&& topLevelAccessControlMap.size() > 0) {
 					AccessSection accessSection = new AccessSection();
 					accessSection.setDocId(docid);
 					AccessSection topLevelAccess = topLevelAccessControlMap.get(docid);
 					accessSection.setPermissionOrder(topLevelAccess.getPermissionOrder());
 					Vector<AccessRule> accessRuleList = topLevelAccess.getAccessRules();
 					for (AccessRule accessRule : accessRuleList) {
 						accessSection.addAccessRule(accessRule);
+					}
 					currentDistributionSection.setAccessSection(accessSection);
+				}
 				if (currentDistributionSection.getAccessSection() != null) {
 					currentDistributionSection.getAccessSection().setDataFileName(currentDistributionSection.getDataFileName());
+				}
 				allDistributionSections.add(currentDistributionSection);
 				currentDistributionSection = null;
 				describesId = null;
 				describesId = new Vector<String>();
+			}
 		} else {
 			// this is in inline part
 			StringBuffer endElement = new StringBuffer();
 			endElement.append("</");
 			endElement.append(qName);
 			endElement.append(">");
 			logMetacat.debug("inline endElement: " + endElement.toString());
 			writeInlineDataIntoFile(inlineDataFileWriter, endElement);
+		}
+	}
             sgarg
-            daigle
+	/**
 	 * SAX Handler that receives notification of comments in the DTD
 	 */
 	public void comment(char[] ch, int start, int length) throws SAXException {
 		logMetacat.debug("COMMENT");
 		if (!handleInlineData) {
 			if (!processingDTD) {
 				DBSAXNode currentNode = (DBSAXNode) nodeStack.peek();
 				String str = new String(ch, start, length);
             sgarg
-            daigle
+				// compare top level access module
-            daigle
+				if (processingTopLevelAccess && needToCheckAccessModule) {
-            daigle
+					compareCommentNode(currentUnchangeableAccessModuleNodeStack, str,
 							UPDATEACCESSERROR);
+				}
 				endNodeId = currentNode.writeChildNodeToDB("COMMENT", null, str, docid);
 				if (needToCheckAccessModule
-            daigle
+						&& (processingAdditionalAccess || processingOtherAccess || processingTopLevelAccess)) {
-            daigle
+					// stored the pull out nodes into storedNode stack
 					NodeRecord nodeElement = new NodeRecord(-2, -2, -2, "COMMENT", null,
-            daigle
+							null, MetacatUtil.normalize(str));
-            daigle
+					storedAccessNodeStack.push(nodeElement);
             sgarg
             daigle
+			}
 		} else {
 			// inline data comment
 			StringBuffer inlineComment = new StringBuffer();
 			inlineComment.append("<!--");
 			inlineComment.append(new String(ch, start, length));
 			inlineComment.append("-->");
 			logMetacat.debug("inline data comment: " + inlineComment.toString());
 			writeInlineDataIntoFile(inlineDataFileWriter, inlineComment);
+		}
+	}
             sgarg
-            daigle
+	/* Compare comment from xml and db */
 	private void compareCommentNode(Stack<NodeRecord> nodeStack, String string,
 			String error) throws SAXException {
 		NodeRecord node = null;
 		try {
 			node = nodeStack.pop();
 		} catch (EmptyStackException ee) {
 			logMetacat.error("the stack is empty for comment data");
 			throw new SAXException(error);
+		}
 		logMetacat.debug("current node type from xml is COMMENT");
 		logMetacat.debug("node type from stack: " + node.getNodeType());
 		logMetacat.debug("current node data from xml is: " + string);
 		logMetacat.debug("node data from stack: " + node.getNodeData());
 		logMetacat.debug("node is from stack: " + node.getNodeId());
 		// if not consistent terminate program and throw a exception
 		if (!node.getNodeType().equals("COMMENT") || !string.equals(node.getNodeData())) {
 			logMetacat.error("Inconsistence happened: ");
 			logMetacat.error("current node type from xml is COMMENT");
 			logMetacat.error("node type from stack: " + node.getNodeType());
 			logMetacat.error("current node data from xml is: " + string);
 			logMetacat.error("node data from stack: " + node.getNodeData());
 			logMetacat.error("node is from stack: " + node.getNodeId());
 			throw new SAXException(error);
 		}// if
+	}
             sgarg
-            daigle
+	/**
 	 * SAX Handler called once for each processing instruction found: node that
 	 * PI may occur before or after the root element.
 	 */
 	public void processingInstruction(String target, String data) throws SAXException {
 		logMetacat.debug("PI");
 		if (!handleInlineData) {
 			DBSAXNode currentNode = (DBSAXNode) nodeStack.peek();
 			endNodeId = currentNode.writeChildNodeToDB("PI", target, data, docid);
 		} else {
 			StringBuffer inlinePI = new StringBuffer();
 			inlinePI.append("<?");
 			inlinePI.append(target);
 			inlinePI.append(" ");
 			inlinePI.append(data);
 			inlinePI.append("?>");
 			logMetacat.debug("inline data pi is: " + inlinePI.toString());
 			writeInlineDataIntoFile(inlineDataFileWriter, inlinePI);
+		}
+	}
             sgarg
-            daigle
+	/** SAX Handler that is called at the start of Namespace */
 	public void startPrefixMapping(String prefix, String uri) throws SAXException {
 		logMetacat.debug("NAMESPACE");
 		if (!handleInlineData) {
 			namespaces.put(prefix, uri);
 		} else {
 			inlineDataNameSpace.put(prefix, uri);
+		}
+	}
             sgarg
-            daigle
+	/**
 	 * SAX Handler that is called for each XML text node that is Ignorable white
 	 * space
 	 */
 	public void ignorableWhitespace(char[] cbuf, int start, int len) throws SAXException {
 		// When validation is turned "on", white spaces are reported here
 		// When validation is turned "off" white spaces are not reported here,
 		// but through characters() callback
 		logMetacat.debug("IGNORABLEWHITESPACE");
 		if (!handleInlineData) {
 			DBSAXNode currentNode = (DBSAXNode) nodeStack.peek();
-            daigle
+				String data = new String(cbuf, start, len);
-            daigle
+				// compare whitespace in access top module
-            daigle
+				if (processingTopLevelAccess && needToCheckAccessModule) {
-            daigle
+					compareWhiteSpace(currentUnchangeableAccessModuleNodeStack, data,
 							UPDATEACCESSERROR);
+				}
 				// Write the content of the node to the database
 				if (needToCheckAccessModule
-            daigle
+						&& (processingAdditionalAccess || processingOtherAccess || processingTopLevelAccess)) {
-            daigle
+					// stored the pull out nodes into storedNode stack
 					NodeRecord nodeElement = new NodeRecord(-2, -2, -2, "TEXT", null,
-            daigle
+							null, MetacatUtil.normalize(data));
-            daigle
+					storedAccessNodeStack.push(nodeElement);
             sgarg
             daigle
 				endNodeId = currentNode.writeChildNodeToDB("TEXT", null, data, docid);
 		} else {
 			// This is inline data write to file directly
 			StringBuffer inlineWhiteSpace = new StringBuffer(new String(cbuf, start, len));
 			writeInlineDataIntoFile(inlineDataFileWriter, inlineWhiteSpace);
+		}
             sgarg
             daigle
             sgarg
-            daigle
+	/* Compare whitespace from xml and db */
 	private void compareWhiteSpace(Stack<NodeRecord> nodeStack, String string,
 			String error) throws SAXException {
 		NodeRecord node = null;
 		try {
 			node = nodeStack.pop();
 		} catch (EmptyStackException ee) {
 			logMetacat.error("the stack is empty for whitespace data");
 			throw new SAXException(error);
+		}
 		if (!node.getNodeType().equals("TEXT") || !string.equals(node.getNodeData())) {
 			logMetacat.error("Inconsistence happened: ");
 			logMetacat.error("current node type from xml is WHITESPACE TEXT");
 			logMetacat.error("node type from stack: " + node.getNodeType());
 			logMetacat.error("current node data from xml is: " + string);
 			logMetacat.error("node data from stack: " + node.getNodeData());
 			logMetacat.error("node is from stack: " + node.getNodeId());
 			throw new SAXException(error);
 		}// if
+	}
             sgarg
-            daigle
+	/** SAX Handler that receives notification of end of the document */
 	public void endDocument() throws SAXException {
 		logMetacat.debug("end Document");
 		// There are some unchangable subtree didn't be compare
 		// This maybe cause user change the subtree id
 		if (!super.getIsRevisionDoc()) {
 			// write access rule to db
-            leinfelder
+			if (writeAccessRules) {
 				writeAccessRuleToDB();
+			}
-            daigle
+			// delete relation table
 			deleteRelations();
 			// write relations
 			for (int i = 0; i < onlineDataFileIdInRelationVector.size(); i++) {
 				String id = onlineDataFileIdInRelationVector.elementAt(i);
 				writeOnlineDataFileIdIntoRelationTable(id);
+			}
+		}
+	}
             sgarg
-            daigle
+	/* The method to write all access rule into db */
 	private void writeAccessRuleToDB() throws SAXException {
 		// Delete old permssion
-            leinfelder
+		deletePermissionsInAccessTable();
-            daigle
+		// write top leve access rule
 		writeTopLevelAccessRuleToDB();
 		// write additional access rule
 		// writeAdditionalAccessRuleToDB();
 		writeAdditionalAccessRulesToDB();
 	}// writeAccessRuleToDB
             sgarg
-            daigle
+	/* The method to write top level access rule into db. */
 	private void writeTopLevelAccessRuleToDB() throws SAXException {
 		// for top document level
 		AccessSection accessSection = topLevelAccessControlMap.get(docid);
 		boolean top = true;
 		String subSectionId = null;
 		if (accessSection != null) {
 			AccessSection accessSectionObj = accessSection;
             sgarg
-            daigle
+			// if accessSection is not null and is not reference
 			if (accessSectionObj.getReferences() == null) {
-            leinfelder
+				// check for denyFirst permOrder
 				String permOrder = accessSectionObj.getPermissionOrder();
 				if (permOrder.equals(AccessControlInterface.DENYFIRST) && ignoreDenyFirst) {
 					logMetacat.warn("Metacat no longer supports EML 'denyFirst' access rules - ignoring this access block");
 			    	return;
+			    }
-            daigle
+				// write the top level access module into xml_accesssubtree to
 				// store info and then when update to check if the user can
 				// update it or not
 				deleteAccessSubTreeRecord(docid);
 				writeAccessSubTreeIntoDB(accessSectionObj, TOPLEVEL);
             sgarg
-            daigle
+				// write access section into xml_access table
 				writeGivenAccessRuleIntoDB(accessSectionObj, top, subSectionId);
 				// write online data file into xml_access too.
 				// for (int i= 0; i <onlineDataFileIdInTopAccessVector.size();
 				// i++)
 				// {
 				// String id = onlineDataFileIdInTopAccessVector.elementAt(i);
 				// writeAccessRuleForRelatedDataFileIntoDB(accessSectionObj,
 				// id);
 				// }
             sgarg
-            daigle
+			} else {
             sgarg
-            daigle
+				// this is a reference and go trough the vector which contains
 				// all access object
 				String referenceId = accessSectionObj.getReferences();
 				boolean findAccessObject = false;
 				logMetacat.debug("referered id for top access: " + referenceId);
 				for (int i = 0; i < accessObjectList.size(); i++) {
 					AccessSection accessObj = accessObjectList.elementAt(i);
 					String accessObjId = accessObj.getSubTreeId();
-            leinfelder
+					// check for denyFirst permOrder
 					String permOrder = accessObj.getPermissionOrder();
 					if (permOrder.equals(AccessControlInterface.DENYFIRST) && ignoreDenyFirst) {
 						logMetacat.warn("Metacat no longer supports EML 'denyFirst' access rules - ignoring this access block, subtree id: " + accessObjId);
 				    	continue;
+				    }
-            daigle
+					if (referenceId != null && accessObj != null
 							&& referenceId.equals(accessObjId)) {
 						// make sure the user didn't change any thing in this
 						// access moduel
 						// too if user doesn't have all permission
 						if (needToCheckAccessModule) {
             sgarg
-            daigle
+							Stack<NodeRecord> newStack = accessObj
 									.getStoredTmpNodeStack();
 							// revise order
-            daigle
+							newStack = DocumentUtil.reviseStack(newStack);
-            daigle
+							// go throught the vector of
 							// unChangeableAccessSubtreevector
 							// and find the one whose id is as same as
 							// referenceid
 							AccessSection oldAccessObj = getAccessSectionFromUnchangableAccessVector(referenceId);
 							// if oldAccessObj is null something is wrong
 							if (oldAccessObj == null) {
 								throw new SAXException(UPDATEACCESSERROR);
 							}// if
 							else {
 								// Get the node stack from old access obj
 								Stack<NodeRecord> oldStack = oldAccessObj
 										.getSubTreeNodeStack();
 								compareNodeStacks(newStack, oldStack);
 							}// else
 						}// if
 						// write accessobject into db
 						writeGivenAccessRuleIntoDB(accessObj, top, subSectionId);
 						// write online data file into xml_access too.
 						// for (int j= 0; j
 						// <onlineDataFileIdInTopAccessVector.size(); j++)
 						// {
 						// String id =
 						// onlineDataFileIdInTopAccessVector.elementAt(j);
 						// writeAccessRuleForRelatedDataFileIntoDB(accessSectionObj,
 						// id);
 						// }
             sgarg
-            daigle
+						// write the reference access into xml_accesssubtree
 						// too write the top level access module into
 						// xml_accesssubtree to store info and then when update
 						// to check if the user can update it or not
 						deleteAccessSubTreeRecord(docid);
 						writeAccessSubTreeIntoDB(accessSectionObj, TOPLEVEL);
 						writeAccessSubTreeIntoDB(accessObj, SUBTREELEVEL);
 						findAccessObject = true;
 						break;
+					}
 				}// for
 				// if we couldn't find an access subtree id for this reference
 				// id
 				if (!findAccessObject) {
 					throw new SAXException("The referenceid: " + referenceId
 							+ " is not access subtree");
 				}// if
 			}// else
             sgarg
-            daigle
+		}// if
 		else {
 			// couldn't find a access section object
 			logMetacat.warn("couldn't find access control for document: " + docid);
+		}
             sgarg
-            daigle
+	}// writeTopLevelAccessRuletoDB
             sgarg
-            daigle
+	/* Given a subtree id and find the responding access section */
 	private AccessSection getAccessSectionFromUnchangableAccessVector(String id) {
 		AccessSection result = null;
 		// Makse sure the id
 		if (id == null || id.equals("")) {
 			return result;
+		}
 		// go throught vector and find the list
 		for (int i = 0; i < unChangeableAccessSubTreeVector.size(); i++) {
 			AccessSection accessObj = unChangeableAccessSubTreeVector.elementAt(i);
 			if (accessObj.getSubTreeId() != null && (accessObj.getSubTreeId()).equals(id)) {
 				result = accessObj;
 			}// if
 		}// for
 		return result;
 	}// getAccessSectionFromUnchangableAccessVector
             sgarg
-            daigle
+	/* Compare two node stacks to see if they are same */
 	private void compareNodeStacks(Stack<NodeRecord> stack1, Stack<NodeRecord> stack2)
 			throws SAXException {
 		// make sure stack1 and stack2 are not empty
 		if (stack1.isEmpty() || stack2.isEmpty()) {
 			logMetacat.error("Because stack is empty!");
 			throw new SAXException(UPDATEACCESSERROR);
+		}
 		// go throw two stacks and compare every element
 		while (!stack1.isEmpty()) {
 			// Pop an element from stack1
 			NodeRecord record1 = stack1.pop();
 			// Pop an element from stack2(stack 2 maybe empty)
 			NodeRecord record2 = null;
 			try {
 				record2 = stack2.pop();
 			} catch (EmptyStackException ee) {
 				logMetacat.error("Node stack2 is empty but stack1 isn't!");
 				throw new SAXException(UPDATEACCESSERROR);
+			}
 			// if two records are not same throw a exception
 			if (!record1.contentEquals(record2)) {
 				logMetacat.error("Two records from new and old stack are not " + "same!");
 				throw new SAXException(UPDATEACCESSERROR);
 			}// if
 		}// while
             sgarg
-            daigle
+		// now stack1 is empty and we should make sure stack2 is empty too
 		if (!stack2.isEmpty()) {
 			logMetacat
 					.error("stack2 still has some elements while stack " + "is empty! ");
 			throw new SAXException(UPDATEACCESSERROR);
 		}// if
 	}// comparingNodeStacks
             daigle
-            daigle
+	/* The method to write additional access rule into db. */
-            daigle
+	private void writeAdditionalAccessRulesToDB() throws SAXException {
 		// Iterate through every distribution and write access sections for data and inline
 		// types to the database
 		for (DistributionSection distributionSection : allDistributionSections) {
 			// we're only interested in data and inline distributions
 			int distributionType = distributionSection.getDistributionType();
 			if (distributionType == DistributionSection.DATA_DISTRIBUTION
 					|| distributionType == DistributionSection.INLINE_DATA_DISTRIBUTION) {
 				AccessSection accessSection = distributionSection.getAccessSection();
 				// If the distribution doesn't have an access section, we continue.
 				if (accessSection == null) {
 					continue;
             leinfelder
             daigle
-            leinfelder
+				// check for denyFirst permOrder
 				String permOrder = accessSection.getPermissionOrder();
 				if (permOrder.equals(AccessControlInterface.DENYFIRST) && ignoreDenyFirst) {
 					logMetacat.warn("Metacat no longer supports EML 'denyFirst' access rules - ignoring this access block: " + distributionSection.getDataFileName());
 			    	continue;
+			    }
-            daigle
+				// We want to check file permissions for all online data updates and inserts, or for
 				// inline updates.
 //				if (distributionType == DistributionSection.DATA_DISTRIBUTION
 //						|| (distributionType == DistributionSection.INLINE_DATA_DISTRIBUTION && action == "UPDATE")) {
             sgarg
-            daigle
+				if (distributionType == DistributionSection.DATA_DISTRIBUTION) {
 					try {
-            leinfelder
+						// check for the previous version for permissions on update
-            leinfelder
+						// we need to look up the docid from the guid, if we have it
-            leinfelder
+						String dataDocid = distributionSection.getDataFileName();
-            leinfelder
+						try {
 							dataDocid = IdentifierManager.getInstance().getLocalId(dataDocid);
 						} catch (McdbDocNotFoundException mcdbnfe) {
 							// ignore
 							logMetacat.warn("Could not find guid/docid mapping for " + dataDocid);
+						}
-            leinfelder
+						String previousDocid = dataDocid;
 						if (action == "UPDATE") {
 							String docidWithoutRev = DocumentUtil.getDocIdFromString(dataDocid);
 							int latestRevision = DBUtil.getLatestRevisionInDocumentTable(docidWithoutRev);
 							if (latestRevision > 0) {
-            leinfelder
+								previousDocid = docidWithoutRev + PropertyService.getProperty("document.accNumSeparator") + latestRevision;
             leinfelder
+						}
-            leinfelder
+						// check both the previous and current data permissions
 						// see: https://projects.ecoinformatics.org/ecoinfo/issues/5647
-            leinfelder
+						PermissionController controller = new PermissionController(previousDocid);
-            leinfelder
+						PermissionController currentController = new PermissionController(dataDocid);
-            daigle
+						if (AccessionNumber.accNumberUsed(docid)
-            leinfelder
+								&&
 								!(controller.hasPermission(user, groups, "WRITE")
 										|| currentController.hasPermission(user, groups, "WRITE")
+										)
 								) {
 							throw new SAXException(UPDATEACCESSERROR + " id: " + dataDocid);
             daigle
 					} catch (SQLException sqle) {
 						throw new SAXException(
 								"Database error checking user permissions: "
 										+ sqle.getMessage());
 					} catch (Exception e) {
 						throw new SAXException(
 								"General error checking user permissions: "
 										+ e.getMessage());
+					}
 				} else if (distributionType == DistributionSection.INLINE_DATA_DISTRIBUTION && action == "UPDATE") {
 					try {
             leinfelder
 						// check for the previous version for permissions
 						int latestRevision = DBUtil.getLatestRevisionInDocumentTable(docid);
 						String previousDocid =
 							docid + PropertyService.getProperty("document.accNumSeparator") + latestRevision;
 						PermissionController controller = new PermissionController(previousDocid);
             sgarg
-            daigle
+						if (!controller.hasPermission(user, groups, "WRITE")) {
 							throw new SAXException(UPDATEACCESSERROR);
+						}
 					} catch (SQLException sqle) {
 						throw new SAXException(
 								"Database error checking user permissions: "
 										+ sqle.getMessage());
 					} catch (Exception e) {
 						throw new SAXException(
 								"General error checking user permissions: "
 										+ e.getMessage());
+					}
+				}
-            leinfelder
+				// clear previous versions first
 				deleteAccessRule(accessSection, false);
 				// now write the new ones
-            daigle
+				String subSectionId = Integer.toString(distributionSection.getDistributionId());
 				writeGivenAccessRuleIntoDB(accessSection, false, subSectionId);
+			}
             sgarg
             daigle
+	}
             leinfelder
 	/**
 	 *  delete existing access for given access rule
+	 *
 	 */
 	private void deleteAccessRule(AccessSection accessSection, boolean topLevel) throws SAXException {
 		if (accessSection == null) {
 			throw new SAXException("The access object is null");
+		}
 		PreparedStatement pstmt = null;
             sgarg
-            leinfelder
+		String sql = null;
 		sql = "DELETE FROM xml_access WHERE guid = ?";
 		try {
 			pstmt = connection.prepareStatement(sql);
 			// Increase DBConnection usage count
 			connection.increaseUsageCount(1);
 			// Bind the values to the query
 			String guid = null;
 			if (topLevel) {
 				try {
 					guid = IdentifierManager.getInstance().getGUID(docid, Integer.valueOf(revision));
 				} catch (NumberFormatException e) {
 					throw new SAXException(e.getMessage(), e);
 				} catch (McdbDocNotFoundException e) {
 					// register the default mapping now
 					guid = docid + "." + revision;
 					IdentifierManager.getInstance().createMapping(guid, guid);
+				}
 			} else {
 				guid = accessSection.getDataFileName();
+			}
 			pstmt.setString(1, guid);
 			logMetacat.debug("guid in accesstable: " + guid);
 			logMetacat.debug("running sql: " + pstmt.toString());
 			pstmt.execute();
 			pstmt.close();
 		}// try
 		catch (SQLException e) {
 			throw new SAXException("EMLSAXHandler.deleteAccessRule(): "
 					+ e.getMessage());
 		}// catch
 		finally {
 			try {
 				pstmt.close();
 			} catch (SQLException ee) {
 				throw new SAXException("EMLSAXHandler.deleteAccessRule(): "
 						+ ee.getMessage());
+			}
 		}// finally
+	}
-            daigle
+	/* Write a given access rule into db */
 	private void writeGivenAccessRuleIntoDB(AccessSection accessSection,
 			boolean topLevel, String subSectionId) throws SAXException {
 		if (accessSection == null) {
 			throw new SAXException("The access object is null");
+		}
             sgarg
-            leinfelder
+		String guid = null;
-            leinfelder
+		String referencedGuid = accessSection.getDataFileName();
-            leinfelder
+		try {
 			guid = IdentifierManager.getInstance().getGUID(docid, Integer.valueOf(revision));
 		} catch (NumberFormatException e) {
 			throw new SAXException(e.getMessage(), e);
 		} catch (McdbDocNotFoundException e) {
 			// register the default mapping now
 			guid = docid + "." + revision;
 			IdentifierManager.getInstance().createMapping(guid, guid);
+		}
-            daigle
+		String permOrder = accessSection.getPermissionOrder();
-            leinfelder
+		String sql = null;
 		PreparedStatement pstmt = null;
-            daigle
+		if (topLevel) {
-            leinfelder
+			sql = "INSERT INTO xml_access (guid, principal_name, permission, "
-            leinfelder
+					+ "perm_type, perm_order, accessfileid) VALUES "
 					+ " (?, ?, ?, ?, ?, ?)";
-            daigle
+		} else {
-            leinfelder
+			sql = "INSERT INTO xml_access (guid,principal_name, "
-            leinfelder
+					+ "permission, perm_type, perm_order, accessfileid, subtreeid"
 					+ ") VALUES" + " (?, ?, ?, ?, ?, ?, ?)";
             daigle
 		try {
             sgarg
-            leinfelder
+			pstmt = connection.prepareStatement(sql);
 			// Increase DBConnection usage count
 			connection.increaseUsageCount(1);
 			// Bind the values to the query
-            leinfelder
+			pstmt.setString(6, guid);
 			logMetacat.debug("Accessfileid in accesstable: " + guid);
-            leinfelder
+			pstmt.setString(5, permOrder);
 			logMetacat.debug("PermOder in accesstable: " + permOrder);
 			// if it is not top level, set subsection id
 			if (topLevel) {
-            leinfelder
+				pstmt.setString(1, guid);
 				logMetacat.debug("Guid in accesstable: " + guid);
             leinfelder
 			if (!topLevel) {
-            leinfelder
+				// use the referenced guid
 				pstmt.setString(1, referencedGuid );
-            leinfelder
+				logMetacat.debug("Docid in accesstable: " + inlineDataFileName);
 				// for subtree should specify the
 				if (subSectionId == null) {
 					throw new SAXException("The subsection is null");
+				}
 				pstmt.setString(7, subSectionId);
 				logMetacat.debug("SubSectionId in accesstable: " + subSectionId);
             slaughter
 				// Save guid of data object for syncing of access policy with CN after parsing
 				// is successful (see DocumentImpl.write)
 				guidsToSync.add(referencedGuid);
             leinfelder
-            daigle
+			Vector<AccessRule> accessRules = accessSection.getAccessRules();
 			// go through every rule
 			for (int i = 0; i < accessRules.size(); i++) {
 				AccessRule rule = accessRules.elementAt(i);
 				String permType = rule.getPermissionType();
 				int permission = rule.getPermission();
-            leinfelder
+				pstmt.setInt(3, permission);
-            daigle
+				logMetacat.debug("permission in accesstable: " + permission);
-            leinfelder
+				pstmt.setString(4, permType);
-            daigle
+				logMetacat.debug("Permtype in accesstable: " + permType);
 				// go through every principle in rule
 				Vector<String> nameVector = rule.getPrincipal();
 				for (int j = 0; j < nameVector.size(); j++) {
 					String prName = nameVector.elementAt(j);
-            leinfelder
+					pstmt.setString(2, prName);
-            daigle
+					logMetacat.debug("Principal in accesstable: " + prName);
-            leinfelder
+					logMetacat.debug("running sql: " + pstmt.toString());
 					pstmt.execute();
-            daigle
+				}// for
 			}// for
-            leinfelder
+			pstmt.close();
-            daigle
+		}// try
-            leinfelder
+		catch (SQLException e) {
-            daigle
+			throw new SAXException("EMLSAXHandler.writeAccessRuletoDB(): "
 					+ e.getMessage());
 		}// catch
-            leinfelder
+		finally {
 			try {
 				pstmt.close();
 			} catch (SQLException ee) {
 				throw new SAXException("EMLSAXHandler.writeAccessRuletoDB(): "
 						+ ee.getMessage());
+			}
 		}// finally
             leinfelder
 		// for D1, refresh the entries
 		HazelcastService.getInstance().refreshSystemMetadataEntry(guid);
 		HazelcastService.getInstance().refreshSystemMetadataEntry(referencedGuid);
             sgarg
-            daigle
+	}// writeGivenAccessRuleIntoDB
             sgarg
-            leinfelder
+	/* Delete from db all permission for resources related to the document, if any */
 	private void deletePermissionsInAccessTable() throws SAXException {
-            leinfelder
+		PreparedStatement pstmt = null;
-            daigle
+		try {
             leinfelder
-            leinfelder
+			String sql = "DELETE FROM xml_access " +
-            leinfelder
+					// the file defines access for another file
 					"WHERE accessfileid IN " +
 						"(SELECT guid from identifier where docid = ? and rev = ?) " +
 					// the described file has other versions describing it
 					"OR guid IN " +
 						"(SELECT xa.guid from xml_access xa, identifier id" +
 						" WHERE xa.accessfileid = id.guid " +
 						" AND id.docid = ?" +
 						" AND id.rev = ?)";
-            daigle
+			// delete all acl records for resources related to @aclid if any
-            leinfelder
+			pstmt = connection.prepareStatement(sql);
-            leinfelder
+			pstmt.setString(1, docid);
 			pstmt.setInt(2, Integer.valueOf(revision));
-            leinfelder
+			// second part of query
 			pstmt.setString(3, docid);
 			pstmt.setInt(4, Integer.valueOf(revision));
-            daigle
+			// Increase DBConnection usage count
 			connection.increaseUsageCount(1);
-            leinfelder
+			logMetacat.debug("running sql: " + sql);
 			pstmt.execute();
             daigle
 		} catch (SQLException e) {
 			throw new SAXException(e.getMessage());
 		} finally {
 			try {
-            leinfelder
+				pstmt.close();
-            daigle
+			} catch (SQLException ee) {
 				throw new SAXException(ee.getMessage());
+			}
+		}
 	}// deletePermissionsInAccessTable
 	/*
 	 * In order to make sure only usr has "all" permission can update access
 	 * subtree in eml document we need to keep access subtree info in
 	 * xml_accesssubtree table, such as docid, version, startnodeid, endnodeid
 	 */
 	private void writeAccessSubTreeIntoDB(AccessSection accessSection, String level)
 			throws SAXException {
 		if (accessSection == null) {
 			throw new SAXException("The access object is null");
+		}
 		String sql = null;
 		PreparedStatement pstmt = null;
 		sql = "INSERT INTO xml_accesssubtree (docid, rev, controllevel, "
 				+ "subtreeid, startnodeid, endnodeid) VALUES " + " (?, ?, ?, ?, ?, ?)";
 		try {
 			pstmt = connection.prepareStatement(sql);
 			// Increase DBConnection usage count
 			connection.increaseUsageCount(1);
 			long startNodeId = accessSection.getStartNodeId();
 			long endNodeId = accessSection.getEndNodeId();
 			String sectionId = accessSection.getSubTreeId();
 			// Bind the values to the query
 			pstmt.setString(1, docid);
 			logMetacat.debug("Docid in access-subtreetable: " + docid);
 			pstmt.setLong(2, (new Long(revision)).longValue());
 			logMetacat.debug("rev in accesssubtreetable: " + revision);
 			pstmt.setString(3, level);
 			logMetacat.debug("contorl level in access-subtree table: " + level);
 			pstmt.setString(4, sectionId);
 			logMetacat.debug("Subtree id in access-subtree table: " + sectionId);
 			pstmt.setLong(5, startNodeId);
 			logMetacat.debug("Start node id is: " + startNodeId);
 			pstmt.setLong(6, endNodeId);
 			logMetacat.debug("End node id is: " + endNodeId);
 			logMetacat.debug("running sql: " + pstmt.toString());
 			pstmt.execute();
 			pstmt.close();
 		}// try
 		catch (SQLException e) {
 			throw new SAXException("EMLSAXHandler.writeAccessSubTreeIntoDB(): "
 					+ e.getMessage());
 		}// catch
 		finally {
 			try {
 				pstmt.close();
 			} catch (SQLException ee) {
 				throw new SAXException("EMLSAXHandler.writeAccessSubTreeIntoDB(): "
 						+ ee.getMessage());
+			}
 		}// finally
 	}// writeAccessSubtreeIntoDB
 	/* Delete every access subtree record from xml_accesssubtree. */
 	private void deleteAccessSubTreeRecord(String docId) throws SAXException {
-            leinfelder
+		PreparedStatement pstmt = null;
-            daigle
+		try {
-            leinfelder
+			String sql = "DELETE FROM xml_accesssubtree WHERE docid = ?";
-            daigle
+			// delete all acl records for resources related to @aclid if any
-            leinfelder
+			pstmt = connection.prepareStatement(sql);
 			pstmt.setString(1, docId);
-            daigle
+			// Increase DBConnection usage count
 			connection.increaseUsageCount(1);
-            leinfelder
+			logMetacat.debug("running sql: " + sql);
 			pstmt.execute();
             daigle
 		} catch (SQLException e) {
 			throw new SAXException(e.getMessage());
 		} finally {
 			try {
-            leinfelder
+				pstmt.close();
-            daigle
+			} catch (SQLException ee) {
 				throw new SAXException(ee.getMessage());
+			}
+		}
 	}// deleteAccessSubTreeRecord
 	// open a file writer for writing inline data to file
-            leinfelder
+	private Writer createInlineDataFileWriter(String fileName, String encoding) throws SAXException {
 		Writer writer = null;
-            daigle
+		String path;
 		try {
 			path = PropertyService.getProperty("application.inlinedatafilepath");
 		} catch (PropertyNotFoundException pnfe) {
 			throw new SAXException(pnfe.getMessage());
+		}
 		/*
 		 * File inlineDataDirectory = new File(path);
 		 */
 		String newFile = path + "/" + fileName;
 		logMetacat.debug("inline file name: " + newFile);
 		try {
 			// true means append
-            leinfelder
+			writer = new OutputStreamWriter(new FileOutputStream(newFile, true), encoding);
-            daigle
+		} catch (IOException ioe) {
 			throw new SAXException(ioe.getMessage());
+		}
 		return writer;
+	}
 	// write inline data into file system and return file name(without path)
-            leinfelder
+	private void writeInlineDataIntoFile(Writer writer, StringBuffer data)
-            daigle
+			throws SAXException {
 		try {
 			writer.write(data.toString());
 			writer.flush();
 		} catch (Exception e) {
 			throw new SAXException(e.getMessage());
+		}
+	}
             daigle
             sgarg
-            daigle
+	// if xml file failed to upload, we need to call this method to delete
 	// the inline data already in file system
 	public void deleteInlineFiles() throws SAXException {
 		if (!inlineFileIdList.isEmpty()) {
 			for (int i = 0; i < inlineFileIdList.size(); i++) {
 				String fileName = inlineFileIdList.elementAt(i);
 				deleteInlineDataFile(fileName);
+			}
+		}
+	}
             sgarg
-            daigle
+	/* delete the inline data file */
 	private void deleteInlineDataFile(String fileName) throws SAXException {
 		String path;
 		try {
 			path = PropertyService.getProperty("application.inlinedatafilepath");
 		} catch (PropertyNotFoundException pnfe) {
 			throw new SAXException("Could not find inline data file path: "
 					+ pnfe.getMessage());
+		}
 		File inlineDataDirectory = new File(path);
 		File newFile = new File(inlineDataDirectory, fileName);
 		newFile.delete();
             sgarg
             daigle
             sgarg
-            daigle
+	/* Delete relations */
 	private void deleteRelations() throws SAXException {
 		PreparedStatement pStmt = null;
 		String sql = "DELETE FROM xml_relation where docid =?";
 		try {
 			pStmt = connection.prepareStatement(sql);
 			// bind variable
 			pStmt.setString(1, docid);
 			// execute query
 			pStmt.execute();
 			pStmt.close();
 		}// try
 		catch (SQLException e) {
 			throw new SAXException("EMLSAXHandler.deleteRelations(): " + e.getMessage());
 		}// catch
 		finally {
 			try {
 				pStmt.close();
 			}// try
 			catch (SQLException ee) {
 				throw new SAXException("EMLSAXHandler.deleteRelations: "
 						+ ee.getMessage());
 			}// catch
 		}// finally
+	}
             sgarg
-            daigle
+	/*
 	 * Write an online data file id into xml_relation table. The dataId
 	 * shouldnot have the revision
 	 */
 	private void writeOnlineDataFileIdIntoRelationTable(String dataId)
 			throws SAXException {
 		PreparedStatement pStmt = null;
 		String sql = "INSERT into xml_relation (docid, packagetype, subject, "
 				+ "relationship, object) values (?, ?, ?, ?, ?)";
 		try {
 			pStmt = connection.prepareStatement(sql);
 			// bind variable
 			pStmt.setString(1, docid);
-            leinfelder
+			pStmt.setString(2, doctype); //DocumentImpl.EML2_1_0NAMESPACE);
-            daigle
+			pStmt.setString(3, docid);
 			pStmt.setString(4, RELATION);
 			pStmt.setString(5, dataId);
 			// execute query
 			pStmt.execute();
 			pStmt.close();
 		}// try
 		catch (SQLException e) {
 			throw new SAXException(
 					"EMLSAXHandler.writeOnlineDataFileIdIntoRelationTable(): "
 							+ e.getMessage());
 		}// catch
 		finally {
 			try {
 				pStmt.close();
 			}// try
 			catch (SQLException ee) {
 				throw new SAXException(
 						"EMLSAXHandler.writeOnlineDataFileIdIntoRelationTable(): "
 								+ ee.getMessage());
 			}// catch
 		}// finally
             sgarg
-            daigle
+	}// writeOnlineDataFileIdIntoRelationTable
             sgarg
-            daigle
+	/*
 	 * This method will handle data file in online url. If the data file is in
 	 * ecogrid protocol, then the datafile identifier(without rev)should be put
 	 * into onlineDataFileRelationVector. The docid in this vector will be
 	 * insert into xml_relation table in endDocument(). If the data file doesn't
 	 * exsit in xml_documents or xml_revision table, or the user has all
 	 * permission to the data file if the docid already existed, the data file
 	 * id (without rev)will be put into onlineDataFileTopAccessVector. The top
 	 * access rules specified in this eml document will apply to the data file.
 	 * NEED to do: We should also need to implement http and ftp. Those external
 	 * files should be download and assign a data file id to it.
 	 */
 	private void handleOnlineUrlDataFile(String url) throws SAXException {
 		logMetacat.warn("The url is " + url);
             sgarg
-            daigle
+		if (currentDistributionSection == null) {
 			throw new SAXException("Trying to set the online file name for a null"
 					+ " distribution section");
+		}
 		// if the url is not in ecogrid protocol, null will be returned
-            daigle
+		String accessionNumber = DocumentUtil.getAccessionNumberFromEcogridIdentifier(url);
             leinfelder
 		// check he accession number and get docid.rev if we can
 		String docid = null;
 		int rev = 0;
 		if (accessionNumber != null) {
 			// get rid of revision number to get the docid.
 			try {
 				docid = DocumentUtil.getDocIdFromAccessionNumber(accessionNumber);
 				rev = DocumentUtil.getRevisionFromAccessionNumber(accessionNumber);
 			} catch (Exception e) {
 				logMetacat.warn(e.getClass().getName() + " - Problem parsing accession number for: " + accessionNumber + ". Message: " + e.getMessage());
 				accessionNumber = null;
+			}
+		}
-            daigle
+		if (accessionNumber == null) {
 			// the accession number is null if the url does not references a
 			// local data file (url would start with "ecogrid://"
 			currentDistributionSection
 					.setDistributionType(DistributionSection.ONLINE_DATA_DISTRIBUTION);
 		} else {
-            leinfelder
+			// look up the guid using docid/rev
-            leinfelder
+			String guid = null;
 			try {
 				guid = IdentifierManager.getInstance().getGUID(docid, rev);
 			} catch (McdbDocNotFoundException e1) {
-            leinfelder
+				// no need to do this if we are not writing access rules for the data
 				if (!writeAccessRules) {
 					logMetacat.warn("Not configured to write access rules for data referenced by: " + url);
 					return;
+				}
-            leinfelder
+				guid = docid + "." + rev;
 				IdentifierManager.getInstance().createMapping(guid, guid);
+			}
             daigle
 			currentDistributionSection
 					.setDistributionType(DistributionSection.DATA_DISTRIBUTION);
-            leinfelder
+			currentDistributionSection.setDataFileName(guid);
             daigle
 			// distributionOnlineFileName = docid;
-            leinfelder
+			onlineDataFileIdInRelationVector.add(guid);
-            daigle
+			try {
-            daigle
+				if (!AccessionNumber.accNumberUsed(docid)) {
-            leinfelder
+					onlineDataFileIdInTopAccessVector.add(guid);
-            daigle
+				} else {
-            leinfelder
+					// check the previous revision if we have it
 					int previousRevision = rev;
 					Vector<Integer> revisions = DBUtil.getRevListFromRevisionTable(docid);
 					if (revisions != null && revisions.size() > 0) {
 						previousRevision = revisions.get(revisions.size() - 1);
+					}
 					String previousDocid =
 						docid + PropertyService.getProperty("document.accNumSeparator") + previousRevision;
             leinfelder
 					// check EITHER previous or current id for access rules
 					// see: https://projects.ecoinformatics.org/ecoinfo/issues/5647
 					PermissionController previousController = new PermissionController(previousDocid);
 					PermissionController currentController = new PermissionController(accessionNumber);
 					if (previousController.hasPermission(user, groups, AccessControlInterface.ALLSTRING)
 							|| currentController.hasPermission(user, groups, AccessControlInterface.ALLSTRING)
 							) {
-            leinfelder
+						onlineDataFileIdInTopAccessVector.add(guid);
-            daigle
+					} else {
 						throw new SAXException(UPDATEACCESSERROR);
+					}
+				}
-            daigle
+			}// try
 			catch (Exception e) {
 				logMetacat.error("Eorr in "
 								+ "Eml210SAXHanlder.handleOnlineUrlDataFile is "
 								+ e.getMessage());
 				throw new SAXException(e.getMessage());
+			}
+		}
+	}
             sgarg

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