/**
* '$RCSfile$'
* 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: Jing Tao
*
* '$Author$'
* '$Date$'
* '$Revision$'
*
* 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.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.Reader;
import java.io.Writer;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.Date;
import java.util.EmptyStackException;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.Stack;
import java.util.Vector;
import org.apache.log4j.Logger;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
import edu.ucsb.nceas.utilities.access.AccessControlInterface;
import edu.ucsb.nceas.metacat.accesscontrol.AccessRule;
import edu.ucsb.nceas.metacat.accesscontrol.AccessSection;
import edu.ucsb.nceas.metacat.database.DBConnection;
import edu.ucsb.nceas.metacat.database.DBConnectionPool;
import edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService;
import edu.ucsb.nceas.metacat.properties.PropertyService;
import edu.ucsb.nceas.metacat.util.AuthUtil;
import edu.ucsb.nceas.metacat.util.DocumentUtil;
import edu.ucsb.nceas.metacat.util.MetacatUtil;
import edu.ucsb.nceas.utilities.PropertyNotFoundException;
/**
* A database aware Class implementing callback methods for the SAX parser to
* call when processing the XML stream and generating events
* Here is the rules for user which has write permission in top level access
* rules(he can update metadata but can't update access module) try to update
* a document:
* 1. Checking access part (both in top level and additional level, node by node)
* If something was modified, reject the document. Note: for additional part
* The access subtree startnode starts at "<describe>" rather than <access>.
* This is because make sure ids wouldn't be mess up by user.
* 2. Checking ids in additional access part, if they points a distribution
* module with online or inline. If some ids don't, reject the documents.
* 3. For inline distribution:
* If user can't read the inline data, the empty string in inline element
* will be send to user if he read this eml document(user has read access
* at top level - metadata, but user couldn't read inline data).
* Here is some interested scenario: If user does have read and write
* permission in top level access rules(for metadata)
* but 1) user doesn't have read and write permission in inline data block,
* so if user update the document with some inline data rather than
* empty string in same inline data block(same distribution inline id),
* this means user updated the inline data. So the document should be
* rejected.
* 2) user doesn't have read permission, but has write permission in
* inline data block. If user send back inline data block with empty
* string, we will think user doesn't update inline data and we will
* copy old inline data back to the new one. If user send something
* else, we will overwrite the old inline data by new one.
* 4. For online distribution:
* It is easy than inline distribution. When the user try to change a external
* document id, we will checking if the user have "all" permission to it.
* If don't have, reject the document. If have, delete the old rules and apply
* The new rules.
*
*
* Here is some info about additional access rules ( data object rules):
* The data access rules format looks like:
* <additionalMetadata>
* <describes>100</describes>
* <describes>300</describes>
* <access>rulesone</access>
* </additionalMetadata>
* <additionalMetadata>
* <describes>200</describes>
* <access>rulesthree</access>
* </additionalMetadata>
* Because eml additionalMetadata is (describes+, any) and any ocurrence is 1.
* So following xml will be rejected by xerces.
* <additionalMetadata>
* <describes>100</describes>
* <describes>300</describes>
* <other>....</other>
* <access>rulesone</access>
* </additionalMetadata>
*/
public class Eml200SAXHandler extends DBSAXHandler implements
AccessControlInterface
{
// Boolean that tells whether we are processing top level (document level) access.
// this is true when we hit an 'access' element, and the grandparent element is
// 'eml' and we are not inside an 'additionalMetadata' section. Set back to false
// in endElement
private boolean processTopLevelAccess = false;
// now additionalAccess will be explained as distribution access control
// - data file
private boolean processAdditionalAccess = false;
// Boolean that tells whether we are processing other access. This is true when
// we find an 'access' element inside an 'additionalMetadata' element. Set back
// to false in endElement
private boolean processOtherAccess = false;
private Vector<String> guidsToSync;
// if we are inside an 'access' element, we use this object to hold the
// current access info
private AccessSection accessObject = null;
// for each 'access/allow' and 'access/deny' we create a new access Rule to hold
// the info
private AccessRule accessRule = null;
private Vector describesId = new Vector(); // store the ids in
//additionalmetadata/describes
//store all distribution element id for online url. key is the distribution
// id and data is url
private Hashtable onlineURLDistributionIdList = new Hashtable();
// distribution/oneline/url will store this vector if distribution doesn't
// have a id.
private Vector onlineURLDistributionListWithoutId = new Vector();
//store all distribution element id for online other distribution, such as
// connection or connectiondefination. key is the distribution id
// and data is distribution id
private Hashtable onlineOtherDistributionIdList = new Hashtable();
//store all distribution element id for inline data.
// key is the distribution id, data is the internal inline id
private Hashtable inlineDistributionIdList = new Hashtable();
//store all distribution element id for off line data.
// key is the distribution id, data is the id too.
private Hashtable offlineDistributionIdList = new Hashtable();
// a hash to stored all distribution id, both key and value are id itself
private Hashtable distributionAllIdList = new Hashtable();
// temporarily store distribution id
private String distributionId = null;
// flag to indicate to handle distribution
private boolean proccessDistribution = false;
// a hash table to stored the distribution which is a reference and this
// distribution has a id too. The key is itself id of this distribution,
// the value is the referenced id.
// So, we only stored the format like this:
// <distribution id ="100"><reference>300</reference></distribution>
// the reason is:
// if not id in distribution, then the distribution couldn't be added
// to additional access module. The distribution block which was referenced
// id (300) will be stored in above distribution lists.
private Hashtable distributionReferenceList = new Hashtable();
// if the action is update and the user does not have ALL permission
// and the user is not an administrator, then we will need to compare
// access modules to make sure the user has update permissions
private boolean needToCheckAccessModule = false;
private AccessSection topAccessSubTreeFromDB = null;
private Vector additionalAccessSubTreeListFromDB = new Vector();
private Hashtable referencedAccessSubTreeListFromDB = new Hashtable();
// this holds the top level (document level) access section.
private AccessSection topAccessSection;
private Vector additionalAccessVector = new Vector();
// key is subtree id and value is accessSection object
private Hashtable possibleReferencedAccessHash = new Hashtable();
// we need an another stack to store the access node which we pull out just
// from xml. If a reference happend, we can use the stack the compare nodes
private Stack storedAccessNodeStack = new Stack();
// vector stored the data file id which will be write into relation table
private Vector onlineDataFileIdInRelationVector = new Vector();
// Indicator of inline data
private boolean handleInlineData = false;
private Hashtable inlineDataNameSpace = null;
private Writer inlineDataFileWriter = null;
private String inlineDataFileName = null;
private int inLineDataIndex = 0;
private Vector inlineFileIDList = new Vector();
private boolean inAdditionalMetaData = false;
//user has unwritable inline data object when it updates a document
private boolean unWritableInlineDataObject = false;
//user has unreadable inline data when it updates a dcoument
private boolean unReadableInlineDataObject = false;
// the hashtable contains the info from xml_access table which
// inline data the user can't read when user update a document.
// The key in hashtable is subtree id and data is the inline data internal
// file name.
private Hashtable previousUnreadableInlineDataObjectHash = new Hashtable();
// the hashtable contains the info from xml_access table which
// inline data the user can't write when user update a document.
// The key in hashtable is subtree id and data is the inline data internal
// file name.
private Hashtable previousUnwritableInlineDataObjectHash = new Hashtable();
private Hashtable accessSubTreeAlreadyWriteDBList = new Hashtable();
//This hashtable will stored the id which already has additional access
// control. So the top level access control will ignore them.
private Hashtable onlineURLIdHasadditionalAccess = new Hashtable();
// additional access module will be in additionalMetadata part. Its format
// look like
//<additionalMetadata>
// <describes>100</describes>
// <describes>300</describes>
// <access>rulesone</access>
//</additionalMetadata>
// If user couldn't have all permission to update access rules, he/she could
// not update access module, but also couldn't update "describes".
// So the start node id for additional access section is the first describes
// element
private boolean firstDescribesInAdditionalMetadata = true;
private long firstDescribesNodeId = -1;
private int numberOfHitUnWritableInlineData = 0;
// Constant
private static final String EML = "eml";
private static final String DESCRIBES = "describes";
private static final String ADDITIONALMETADATA = "additionalMetadata";
private static final String ORDER = "order";
private static final String ID = "id";
private static final String REFERENCES = "references";
public static final String INLINE = "inline";
private static final String ONLINE = "online";
private static final String OFFLINE = "offline";
private static final String CONNECTION = "connection";
private static final String CONNECTIONDEFINITION = "connectionDefinition";
private static final String URL = "url";
private static final String PERMISSIONERROR = "User tried to update a subtree "
+ "when they don't have write permission!";
private static final String UPDATEACCESSERROR = "User tried to update an "
+ "access module when they don't have \"ALL\" permission on the object ";
public static final String TOPLEVEL = "top";
public static final String DATAACCESSLEVEL = "dataAccess";
// this level is for the access module which is not in top or additional
// place, but it was referenced by top or additional
private static final String REFERENCEDLEVEL = "referenced";
private static final String RELATION = "Provides info for";
private static final String DISTRIBUTION = "distribution";
private Logger logMetacat = Logger.getLogger(Eml200SAXHandler.class);
/**
* Construct an instance of the handler class In this constructor, user can
* specify the version need to upadate
*
* @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 Eml200SAXHandler(DBConnection conn, String action, String docid,
String revision, String user, String[] groups, String pub,
int serverCode, Date createDate, Date updateDate, boolean writeAccessRules, Vector<String> guidsToSync) throws SAXException
{
super(conn, action, docid, revision, user, groups, pub,
serverCode, createDate, updateDate, writeAccessRules);
this.guidsToSync = guidsToSync;
// Get the unchangable subtrees (user doesn't have write permission)
try
{
//Here is for data object checking.
if (action != null && action.equals("UPDATE")) {
// 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 the action is update and user doesn't have "ALL" or "CHMOD" permission
// we need to check if user update access subtree
if ( !control.hasPermission(user, groups, AccessControlInterface.ALLSTRING)
&& !control.hasPermission(user, groups, AccessControlInterface.CHMODSTRING)
&& !AuthUtil.isAdministrator(user, groups) && writeAccessRules) {
needToCheckAccessModule = true;
topAccessSubTreeFromDB = getTopAccessSubTreeFromDB();
additionalAccessSubTreeListFromDB =
getAdditionalAccessSubTreeListFromDB();
referencedAccessSubTreeListFromDB =
getReferencedAccessSubTreeListFromDB();
}
//info about inline data object which user doesn't have read
//permission the info come from xml_access table
previousUnreadableInlineDataObjectHash = PermissionController.
getUnReadableInlineDataIdList(previousDocid, user, groups);
//info about data object which user doesn't have write permission
// the info come from xml_accesss table
previousUnwritableInlineDataObjectHash = PermissionController.
getUnWritableInlineDataIdList(previousDocid, user,
groups, true);
}
}
catch (Exception e)
{
logMetacat.error("error in Eml200SAXHandler is " + e.getMessage());
throw new SAXException(e.getMessage());
}
}
/*
* Get the top level access subtree info from xml_accesssubtree table.
* If no top access subtree found, null will be return.
*/
private AccessSection getTopAccessSubTreeFromDB()
throws SAXException
{
AccessSection topAccess = null;
PreparedStatement pstmt = null;
ResultSet rs = null;
String sql = "SELECT subtreeid, startnodeid, endnodeid "
+ "FROM xml_accesssubtree WHERE docid like ? "
+ "AND controllevel like ?";
try
{
pstmt = connection.prepareStatement(sql);
// Increase DBConnection usage count
connection.increaseUsageCount(1);
// Bind the values to the query
pstmt.setString(1, docid);
pstmt.setString(2, TOPLEVEL);
logMetacat.trace("Eml200SAXHandler.getTopAccessSubTreeFromDB - executing SQL: " + pstmt.toString());
pstmt.execute();
// Get result set
rs = pstmt.getResultSet();
if (rs.next())
{
String sectionId = rs.getString(1);
long startNodeId = rs.getLong(2);
long endNodeId = rs.getLong(3);
// create a new access section
topAccess = new AccessSection();
topAccess.setControlLevel(TOPLEVEL);
topAccess.setDocId(docid);
topAccess.setSubTreeId(sectionId);
topAccess.setStartNodeId(startNodeId);
topAccess.setEndNodeId(endNodeId);
}
pstmt.close();
}//try
catch (SQLException e)
{
throw new SAXException(
"EMLSAXHandler.getTopAccessSubTreeFromDB(): "
+ e.getMessage());
}//catch
finally
{
try
{
pstmt.close();
}
catch (SQLException ee)
{
throw new SAXException(
"EMLSAXHandler.getTopAccessSubTreeFromDB(): "
+ ee.getMessage());
}
}//finally
return topAccess;
}
/*
* Get the subtree node info from xml_accesssubtree table
*/
private Vector getAdditionalAccessSubTreeListFromDB() throws Exception
{
Vector result = new Vector();
PreparedStatement pstmt = null;
ResultSet rs = null;
String sql = "SELECT subtreeid, startnodeid, endnodeid "
+ "FROM xml_accesssubtree WHERE docid like ? "
+ "AND controllevel like ? "
+ "ORDER BY startnodeid ASC";
try
{
pstmt = connection.prepareStatement(sql);
// Increase DBConnection usage count
connection.increaseUsageCount(1);
// Bind the values to the query
pstmt.setString(1, docid);
pstmt.setString(2, DATAACCESSLEVEL);
pstmt.execute();
// Get result set
rs = pstmt.getResultSet();
while (rs.next())
{
String sectionId = rs.getString(1);
long startNodeId = rs.getLong(2);
long endNodeId = rs.getLong(3);
// create a new access section
AccessSection accessObj = new AccessSection();
accessObj.setControlLevel(DATAACCESSLEVEL);
accessObj.setDocId(docid);
accessObj.setSubTreeId(sectionId);
accessObj.setStartNodeId(startNodeId);
accessObj.setEndNodeId(endNodeId);
// add this access obj into vector
result.add(accessObj);
}
pstmt.close();
}//try
catch (SQLException e)
{
throw new SAXException(
"EMLSAXHandler.getadditionalAccessSubTreeListFromDB(): "
+ e.getMessage());
}//catch
finally
{
try
{
pstmt.close();
}
catch (SQLException ee)
{
throw new SAXException(
"EMLSAXHandler.getAccessSubTreeListFromDB(): "
+ ee.getMessage());
}
}//finally
return result;
}
/*
* Get the access subtree for referenced info from xml_accesssubtree table
*/
private Hashtable getReferencedAccessSubTreeListFromDB() throws Exception
{
Hashtable result = new Hashtable();
PreparedStatement pstmt = null;
ResultSet rs = null;
String sql = "SELECT subtreeid, startnodeid, endnodeid "
+ "FROM xml_accesssubtree WHERE docid like ? "
+ "AND controllevel like ? "
+ "ORDER BY startnodeid ASC";
try
{
pstmt = connection.prepareStatement(sql);
// Increase DBConnection usage count
connection.increaseUsageCount(1);
// Bind the values to the query
pstmt.setString(1, docid);
pstmt.setString(2, REFERENCEDLEVEL);
pstmt.execute();
// Get result set
rs = pstmt.getResultSet();
while (rs.next())
{
String sectionId = rs.getString(1);
long startNodeId = rs.getLong(2);
long endNodeId = rs.getLong(3);
// create a new access section
AccessSection accessObj = new AccessSection();
accessObj.setControlLevel(DATAACCESSLEVEL);
accessObj.setDocId(docid);
accessObj.setSubTreeId(sectionId);
accessObj.setStartNodeId(startNodeId);
accessObj.setEndNodeId(endNodeId);
// add this access obj into hastable
if ( sectionId != null && !sectionId.trim().equals(""))
{
result.put(sectionId, accessObj);
}
}
pstmt.close();
}//try
catch (SQLException e)
{
throw new SAXException(
"EMLSAXHandler.getReferencedAccessSubTreeListFromDB(): "
+ e.getMessage());
}//catch
finally
{
try
{
pstmt.close();
}
catch (SQLException ee)
{
throw new SAXException(
"EMLSAXHandler.getReferencedSubTreeListFromDB(): "
+ ee.getMessage());
}
}//finally
return result;
}
/** 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.trace("Start ELEMENT(qName) " + qName);
logMetacat.trace("Start ELEMENT(localName) " + localName);
logMetacat.trace("Start ELEMENT(uri) " + uri);
DBSAXNode parentNode = null;
DBSAXNode currentNode = null;
// none inline part
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
if (!handleInlineData)
{
// Get a reference to the parent node for the id
try
{
parentNode = (DBSAXNode) nodeStack.peek();
}
catch (EmptyStackException e)
{
parentNode = null;
}
//start handle inline data
//=====================================================
if (qName.equals(INLINE) && !inAdditionalMetaData)
{
handleInlineData = true;
inLineDataIndex++;
//intitialize namespace hash for in line data
inlineDataNameSpace = new Hashtable();
//initialize file writer
String docidWithoutRev = DocumentUtil.getDocIdFromString(docid);
String seperator = ".";
try {
seperator = PropertyService.getProperty("document.accNumSeparator");
} catch (PropertyNotFoundException pnfe) {
logMetacat.error("Could not get property 'accNumSeparator'. "
+ "Setting separator to '.': "+ pnfe.getMessage());
}
// the new file name will look like docid.rev.2
inlineDataFileName = docidWithoutRev + seperator + revision
+ seperator + inLineDataIndex;
inlineDataFileWriter = createInlineDataFileWriter(inlineDataFileName, encoding);
// put the inline file id into a vector. If upload failed,
// metacat will
// delete the inline data file
inlineFileIDList.add(inlineDataFileName);
// put distribution id and inline file id into a hash
if (distributionId != null)
{
//check to see if this inline data is readable or writable to
// this user
if (!previousUnreadableInlineDataObjectHash.isEmpty() &&
previousUnreadableInlineDataObjectHash.containsKey(distributionId))
{
unReadableInlineDataObject = true;
}
if (!previousUnwritableInlineDataObjectHash.isEmpty() &&
previousUnwritableInlineDataObjectHash.containsKey(distributionId))
{
unWritableInlineDataObject = true;
numberOfHitUnWritableInlineData++;
}
// store the distributid and inlinedata filename into a hash
inlineDistributionIdList.put(distributionId, inlineDataFileName);
}
}
//==============================================================
// If hit a text node, we need write this text for current's parent
// node
// This will happend if the element is mixted
//==============================================================
if (hitTextNode && parentNode != null)
{
if (needToCheckAccessModule
&& (processAdditionalAccess || processOtherAccess || processTopLevelAccess)) {
// 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);
}
// write the textbuffer into db for parent node.
endNodeId = writeTextForDBSAXNode(endNodeId, textBuffer,
parentNode);
// rest hitTextNode
hitTextNode = false;
// reset textbuffer
textBuffer = null;
textBuffer = new StringBuffer();
}
//==================================================================
// 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.info("DOCNAME-a: " + docname);
logMetacat.info("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.info("DOCTYPE-b: " + doctype);
}
rootNode.writeNodename(docname);
//System.out.println("here!!!!!!!!!!!!!!!!!!1");
try {
// for validated XML Documents store a reference to XML DB
// Catalog
// Because this is select statement and it needn't to roll
// back if
// insert document action fialed.
// In order to decrease DBConnection usage count, we get a
// new
// dbconnection from pool
//String catalogid = null;
DBConnection dbConn = null;
int serialNumber = -1;
try {
// Get dbconnection
dbConn = DBConnectionPool
.getDBConnection("DBSAXHandler.startElement");
serialNumber = dbConn.getCheckOutSerialNumber();
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();
boolean hasRow = rs.next();
if (hasRow) {
catalogid = rs.getString(1);
}
pstmt.close();
//System.out.println("here!!!!!!!!!!!!!!!!!!2");
}//try
finally {
// Return dbconnection
DBConnectionPool.returnDBConnection(dbConn,
serialNumber);
}//finally
//create documentImpl object by the constructor which can
// specify
//the revision
if (!super.getIsRevisionDoc())
{
logMetacat.debug("EML200SaxHandler.startElement - creating new DocumentImple for " + docid);
currentDocument = new DocumentImpl(connection, rootNode
.getNodeID(), docname, doctype, docid, revision,
action, user, this.pub, catalogid, this.serverCode,
createDate, updateDate);
}
} catch (Exception ane) {
throw (new SAXException("EML200SaxHandler.startElement - error with action " +
action + " : " + ane.getMessage()));
}
}
//==================================================================
// node
//==================================================================
// 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 discated
long startNodeId = currentNode.getNodeID();
// Add all of the namespaces
String prefix = null;
String nsuri = null;
Enumeration prefixes = namespaces.keys();
while (prefixes.hasMoreElements())
{
prefix = (String) prefixes.nextElement();
nsuri = (String) namespaces.get(prefix);
endNodeId = currentNode.setNamespace(prefix, nsuri, docid);
}
//=================================================================
// attributes
// 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);
// 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 regeistered.
if (attributeName != null
&& attributeName
.indexOf(MetaCatServlet.SCHEMALOCATIONKEYWORD) != -1) {
/*SchemaLocationResolver resolver = new SchemaLocationResolver(
attributeValue);
resolver.resolveNameSpace();*/
}
else if (attributeName != null && attributeName.equals(ID) &&
currentNode.getTagName().equals(DISTRIBUTION) &&
!inAdditionalMetaData)
{
// this is a distribution element and the id is distributionID
distributionId = attributeValue;
distributionAllIdList.put(distributionId, distributionId);
}
}//for
//=================================================================
// handle access stuff
//==================================================================
if (localName.equals(ACCESS))
{
//make sure the access is top level
// this mean current node's parent's parent should be "eml"
DBSAXNode tmpNode = (DBSAXNode) nodeStack.pop();// pop out
// parent
// node
//peek out grandParentNode
DBSAXNode grandParentNode = (DBSAXNode) nodeStack.peek();
// put parent node back
nodeStack.push(tmpNode);
String grandParentTag = grandParentNode.getTagName();
if (grandParentTag.equals(EML) && !inAdditionalMetaData)
{
processTopLevelAccess = true;
}
else if ( !inAdditionalMetaData )
{
// process other access embedded into resource level
// module
processOtherAccess = true;
}
else
{
// this for access in additional data which doesn't have a
// described element. If it has a described element,
// this code won't hurt any thing
processAdditionalAccess = true;
}
// 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);
// for additional access subtree, the start of node id should
// be describe element. We also stored the start access element
// node id too.
if (processAdditionalAccess)
{
accessObject.setStartedDescribesNodeId(firstDescribesNodeId);
accessObject.setControlLevel(DATAACCESSLEVEL);
}
else if (processTopLevelAccess)
{
accessObject.setControlLevel(TOPLEVEL);
}
else if (processOtherAccess)
{
accessObject.setControlLevel(REFERENCEDLEVEL);
}
accessObject.setStartNodeId(startNodeId);
accessObject.setDocId(docid);
}
// Set up a access rule for allow
else if (parentNode.getTagName() != null
&& (parentNode.getTagName()).equals(ACCESS)
&& localName.equals(ALLOW))
{
accessRule = new AccessRule();
//set permission type "allow"
accessRule.setPermissionType(ALLOW);
}
// set up an access rule for den
else if (parentNode.getTagName() != null
&& (parentNode.getTagName()).equals(ACCESS)
&& localName.equals(DENY))
{
accessRule = new AccessRule();
//set permission type "allow"
accessRule.setPermissionType(DENY);
}
//=================================================================
// some other independ stuff
// 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);
// store access module element and attributes into stored stack
if (needToCheckAccessModule
&& (processAdditionalAccess || processOtherAccess || processTopLevelAccess))
{
// stored the pull out nodes into storedNode stack
NodeRecord nodeElement = new NodeRecord(-2, -2, -2, "ELEMENT",
localName, prefix, MetacatUtil.normalize(null));
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", attributeName, null, MetacatUtil
.normalize(attributeValue));
storedAccessNodeStack.push(nodeAttribute);
}
}
if (currentNode.getTagName().equals(ADDITIONALMETADATA))
{
inAdditionalMetaData = true;
}
else if (currentNode.getTagName().equals(DESCRIBES) &&
parentNode.getTagName().equals(ADDITIONALMETADATA) &&
firstDescribesInAdditionalMetadata)
{
// this is first decirbes element in additional metadata
firstDescribesNodeId = startNodeId;
// we started process additional access rules here
// because access and describe couldn't be seperated
NodeRecord nodeElement = new NodeRecord(-2, -2, -2, "ELEMENT",
localName, prefix, MetacatUtil.normalize(null));
storedAccessNodeStack.push(nodeElement);
processAdditionalAccess = true;
logMetacat.info("set processAdditonalAccess true when meet describe");
}
else if (inAdditionalMetaData && processAdditionalAccess &&
parentNode.getTagName().equals(ADDITIONALMETADATA) &&
!currentNode.getTagName().equals(DESCRIBES) &&
!currentNode.getTagName().equals(ACCESS))
{
// we start processadditionalAccess module when first hit describes
// in additionalMetadata. So this is possible, there are
// "describes" but not "access". So here is try to terminate
// processAddionalAccess. In this situation, there another element
// rather than "describes" or "access" as a child of additionalMetadata
// so this is impossible it will have access element now.
// If additionalMetadata has access element, the flag will be
// terminated in endElement
processAdditionalAccess = false;
logMetacat.warn("set processAddtionAccess false if the there is no access in additional");
}
else if (currentNode.getTagName().equals(DISTRIBUTION) &&
!inAdditionalMetaData)
{
proccessDistribution = true;
}
//==================================================================
// reset name space
namespaces = null;
namespaces = new Hashtable();
}//not inline data
// inline data
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
else
{
// we don't buffer the inline data in characters() method
// so start character don't need to hand text node.
// 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 prefixes = inlineDataNameSpace.keys();
while (prefixes.hasMoreElements()) {
prefix = (String) prefixes.nextElement();
nsuri = (String) inlineDataNameSpace.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();
//write inline data into file
logMetacat.info("the inline element data is: "
+ inlineElements.toString());
writeInlineDataIntoFile(inlineDataFileWriter, inlineElements);
}//else
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
}
/** SAX Handler that is called for each XML text node */
public void characters(char[] cbuf, int start, int len) throws SAXException
{
logMetacat.info("CHARACTERS");
if (!handleInlineData) {
// buffer all text nodes for same element. This is for text was
// splited
// 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.info("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);
if (needToCheckAccessModule
&& (processAdditionalAccess || processOtherAccess || processTopLevelAccess))
{
// 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);
}
textBuffer = null;
textBuffer = new StringBuffer();
}
}
else
{
// this is inline data and write file system directly
// we don't need to buffered it.
StringBuffer inlineText = new StringBuffer();
inlineText.append(new String(cbuf, start, len));
logMetacat.info(
"The inline text data write into file system: "
+ inlineText.toString());
writeInlineDataIntoFile(inlineDataFileWriter, inlineText);
}
}
/** SAX Handler that is called at the end of each XML element */
public void endElement(String uri, String localName, String qName)
throws SAXException
{
logMetacat.info("End ELEMENT " + qName);
// when close inline element
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
if (localName.equals(INLINE) && handleInlineData)
{
// Get the node from the stack
DBSAXNode currentNode = (DBSAXNode) nodeStack.pop();
String currentTag = currentNode.getTagName();
logMetacat.info("End of inline data");
// close file writer
try
{
inlineDataFileWriter.close();
handleInlineData = false;
}
catch (IOException ioe)
{
throw new SAXException(ioe.getMessage());
}
//check if user changed inine data or not if user doesn't have
// write permission for this inline block
// if some error happends, we would delete the inline data file here,
// we will call a method named deletedInlineFiles in DocumentImple
if (unWritableInlineDataObject)
{
if (unReadableInlineDataObject)
{
// now user just got a empty string in linline part
// so if the user send back a empty string is fine and we will
// copy the old file to new file. If he send something else,
// the document will be rejected
if (inlineDataIsEmpty(inlineDataFileName))
{
copyInlineFile(distributionId, inlineDataFileName);
}
else
{
logMetacat.info(
"inline data was changed by a user"
+ " who doesn't have permission");
throw new SAXException(PERMISSIONERROR);
}
}//if
else
{
// user get the inline data
if (modifiedInlineData(distributionId, inlineDataFileName))
{
logMetacat.info(
"inline data was changed by a user"
+ " who doesn't have permission");
throw new SAXException(PERMISSIONERROR);
}//if
}//else
}//if
else
{
//now user can update file.
if (unReadableInlineDataObject)
{
// now user just got a empty string in linline part
// so if the user send back a empty string is fine and we will
// copy the old file to new file. If he send something else,
// the new inline data will overwite the old one(here we need
// do nothing because the new inline data already existed
if (inlineDataIsEmpty(inlineDataFileName))
{
copyInlineFile(distributionId, inlineDataFileName);
}
}//if
}//else
// 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();
// resetinlinedata file name
inlineDataFileName = null;
unWritableInlineDataObject = false;
unReadableInlineDataObject = false;
return;
}
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// close element which is not in inline data
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
if (!handleInlineData)
{
// Get the node from the stack
DBSAXNode currentNode = (DBSAXNode) nodeStack.pop();
String currentTag = currentNode.getTagName();
// 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);
}
else if (currentTag.equals(PERMISSION) && accessRule != null)
{
data = (textBuffer.toString()).trim();
// we conbine different a permission into one value
int permission = accessRule.getPermission();
// add permision
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);
}
// put additionalmetadata/describes into vector
else if (currentTag.equals(DESCRIBES))
{
data = (textBuffer.toString()).trim();
describesId.add(data);
//firstDescribesInAdditionalMetadata = false;
//firstDescribesNodeId = 0;
}
else if (currentTag.equals(REFERENCES)
&& (processTopLevelAccess || processAdditionalAccess || processOtherAccess))
{
// get reference
data = (textBuffer.toString()).trim();
// put reference id into accessSection
accessObject.setReferences(data);
}
else if (currentTag.equals(REFERENCES) && proccessDistribution)
{
// get reference for distribution
data = (textBuffer.toString()).trim();
// we only stored the distribution reference which itself
// has a id
if (distributionId != null)
{
distributionReferenceList.put(distributionId, data);
}
}
else if (currentTag.equals(URL) && !inAdditionalMetaData)
{
//handle online data, make sure its'parent is online
DBSAXNode parentNode = (DBSAXNode) nodeStack.peek();
if (parentNode != null && parentNode.getTagName() != null
&& parentNode.getTagName().equals(ONLINE))
{
data = (textBuffer.toString()).trim();
if (distributionId != null)
{
onlineURLDistributionIdList.put(distributionId, data);
}
else
{
onlineURLDistributionListWithoutId.add(data);
}
}//if
}//else if
// write text to db if it is not inline data
logMetacat.info(
"Write text into DB in End Element");
// write text node into db
endNodeId = writeTextForDBSAXNode(endNodeId, textBuffer,
currentNode);
if (needToCheckAccessModule
&& (processAdditionalAccess || processOtherAccess || processTopLevelAccess)) {
// 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);
}
}//if handle text node
//set hitText false
hitTextNode = false;
// reset textbuff
textBuffer = null;
textBuffer = new StringBuffer();
// access stuff
if (currentTag.equals(ALLOW) || currentTag.equals(DENY))
{
// finish parser a ccess 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;
}// ALLOW or DENY
else if (currentTag.equals(ACCESS))
{
// finish parse a access setction and stored them into different
// places
accessObject.setEndNodeId(endNodeId);
AccessSection newAccessObject = accessObject;
newAccessObject.setStoredTmpNodeStack(storedAccessNodeStack);
if (newAccessObject != null)
{
if (processTopLevelAccess)
{
topAccessSection = newAccessObject;
}//if
else if (processAdditionalAccess)
{
// for additional control
// put discribesId into the accessobject and put this
// access object into vector
newAccessObject.setDescribedIdList(describesId);
additionalAccessVector.add(newAccessObject);
}//if
else if (processOtherAccess)
{
// we only stored the access object which has a id
// because only the access object which has a id can
// be reference
if (newAccessObject.getSubTreeId() != null &&
!newAccessObject.getSubTreeId().trim().equals(""))
{
possibleReferencedAccessHash.
put(newAccessObject.getSubTreeId(), newAccessObject);
}
}
}//if
//reset access section object
accessObject = null;
// reset tmp stored node stack
storedAccessNodeStack = null;
storedAccessNodeStack = new Stack();
// reset flag
processAdditionalAccess = false;
processTopLevelAccess = false;
processOtherAccess = false;
}//access element
else if (currentTag.equals(ADDITIONALMETADATA))
{
//reset describesId
describesId = null;
describesId = new Vector();
inAdditionalMetaData = false;
firstDescribesNodeId = -1;
// reset tmp stored node stack
storedAccessNodeStack = null;
storedAccessNodeStack = new Stack();
}
else if (currentTag.equals(DISTRIBUTION) && !inAdditionalMetaData)
{
//reset distribution id
distributionId = null;
proccessDistribution = false;
}
else if (currentTag.equals(OFFLINE) && !inAdditionalMetaData)
{
if (distributionId != null)
{
offlineDistributionIdList.put(distributionId, distributionId);
}
}
else if ((currentTag.equals(CONNECTION) || currentTag.equals(CONNECTIONDEFINITION))
&& !inAdditionalMetaData)
{
//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 (distributionId != null)
{
onlineOtherDistributionIdList.put(distributionId, distributionId);
}
}//if
}//else if
else if (currentTag.equals(DESCRIBES))
{
firstDescribesInAdditionalMetadata = false;
}
}
// close elements which are in inline data (inline data can be xml doc)
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
else
{
// this is in inline part
StringBuffer endElement = new StringBuffer();
endElement.append("</");
endElement.append(qName);
endElement.append(">");
logMetacat.info("inline endElement: "
+ endElement.toString());
writeInlineDataIntoFile(inlineDataFileWriter, endElement);
}
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
}
/*
* Method to check if the new line data is as same as the old one
*/
private boolean modifiedInlineData(String inlineDistributionId,
String newInlineInternalFileName) throws SAXException {
boolean modified = true;
if (inlineDistributionId == null || newInlineInternalFileName == null)
{
return modified;
}
String oldInlineInternalFileName =
(String)previousUnwritableInlineDataObjectHash.get(inlineDistributionId);
if (oldInlineInternalFileName == null ||
oldInlineInternalFileName.trim().equals(""))
{
return modified;
}
logMetacat.info("in handle inline data");
logMetacat.info("the inline data file name from xml_access is: "
+ oldInlineInternalFileName);
try
{
if (!compareInlineDataFiles(oldInlineInternalFileName,
newInlineInternalFileName))
{
modified = true;
}
else
{
modified = false;
}
}
catch(Exception e)
{
modified = true;
}
// delete the inline data file already in file system
if (modified)
{
deleteInlineDataFile(newInlineInternalFileName);
}
return modified;
}
/*
* A method to check if a line file is empty
*/
private boolean inlineDataIsEmpty(String fileName) throws SAXException
{
boolean isEmpty = true;
if ( fileName == null)
{
throw new SAXException("The inline file name is null");
}
try {
String path = PropertyService.getProperty("application.inlinedatafilepath");
// the new file name will look like path/docid.rev.2
File inlineDataDirectory = new File(path);
File inlineDataFile = new File(inlineDataDirectory, fileName);
Reader inlineFileReader = new InputStreamReader(new FileInputStream(inlineDataFile), encoding);
BufferedReader inlineStringReader = new BufferedReader(inlineFileReader);
String string = inlineStringReader.readLine();
// at the end oldstring will be null
while (string != null) {
string = inlineStringReader.readLine();
if (string != null && !string.trim().equals("")) {
isEmpty = false;
break;
}
}
} catch (Exception e) {
throw new SAXException(e.getMessage());
}
return isEmpty;
}
/**
* SAX Handler that receives notification of comments in the DTD
*/
public void comment(char[] ch, int start, int length) throws SAXException
{
logMetacat.info("COMMENT");
if (!handleInlineData) {
if (!processingDTD) {
DBSAXNode currentNode = (DBSAXNode) nodeStack.peek();
String str = new String(ch, start, length);
//compare comment if need
/*if (startCriticalSubTree) {
compareCommentNode(currentUnChangedableSubtreeNodeStack,
str, PERMISSIONERROR);
}//if*/
//compare top level access module
if (processTopLevelAccess && needToCheckAccessModule) {
/*compareCommentNode(currentUnchangableAccessModuleNodeStack,
str, UPDATEACCESSERROR);*/
}
endNodeId = currentNode.writeChildNodeToDB("COMMENT", null,
str, docid);
if (needToCheckAccessModule
&& (processAdditionalAccess || processOtherAccess || processTopLevelAccess)) {
// stored the pull out nodes into storedNode stack
NodeRecord nodeElement = new NodeRecord(-2, -2, -2,
"COMMENT", null, null, MetacatUtil.normalize(str));
storedAccessNodeStack.push(nodeElement);
}
}
} else {
// inline data comment
StringBuffer inlineComment = new StringBuffer();
inlineComment.append("<!--");
inlineComment.append(new String(ch, start, length));
inlineComment.append("-->");
logMetacat.info("inline data comment: "
+ inlineComment.toString());
writeInlineDataIntoFile(inlineDataFileWriter, inlineComment);
}
}
/**
* 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.info("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.info("inline data pi is: "
+ inlinePI.toString());
writeInlineDataIntoFile(inlineDataFileWriter, inlinePI);
}
}
/** SAX Handler that is called at the start of Namespace */
public void startPrefixMapping(String prefix, String uri)
throws SAXException
{
logMetacat.info("NAMESPACE");
logMetacat.info("NAMESPACE prefix "+prefix);
logMetacat.info("NAMESPACE uri "+uri);
if (!handleInlineData) {
namespaces.put(prefix, uri);
} else {
inlineDataNameSpace.put(prefix, uri);
}
}
/**
* 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.info("IGNORABLEWHITESPACE");
if (!handleInlineData) {
DBSAXNode currentNode = (DBSAXNode) nodeStack.peek();
String data = new String(cbuf, start, len);
//compare whitespace in access top module
if (processTopLevelAccess && needToCheckAccessModule) {
/*compareWhiteSpace(currentUnchangableAccessModuleNodeStack,
data, UPDATEACCESSERROR);*/
}
// Write the content of the node to the database
if (needToCheckAccessModule
&& (processAdditionalAccess || processOtherAccess || processTopLevelAccess)) {
// stored the pull out nodes into storedNode stack
NodeRecord nodeElement = new NodeRecord(-2, -2, -2, "TEXT",
null, null, MetacatUtil.normalize(data));
storedAccessNodeStack.push(nodeElement);
}
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);
}
}
/** SAX Handler that receives notification of end of the document */
public void endDocument() throws SAXException
{
logMetacat.info("end Document");
if (needToCheckAccessModule)
{
compareAllAccessModules();
}
// user deleted some inline block which it counldn't delete
if (numberOfHitUnWritableInlineData !=
previousUnwritableInlineDataObjectHash.size())
{
throw new SAXException("user deleted some inline block it couldn't");
}
if (!super.getIsRevisionDoc())
{
// write access rule to xml_access table which include both top level
// and additional level(data access level). It also write access subtree
// info into xml_accesssubtree about the top access, additional access
// and some third place access modules which are referenced by top
// level or additional level
if (writeAccessRules ) {
writeAccessRuleToDB();
}
//delete relation table
deleteRelations();
//write relations
for (int i = 0; i < onlineDataFileIdInRelationVector.size(); i++) {
String id = (String) onlineDataFileIdInRelationVector.elementAt(i);
writeOnlineDataFileIdIntoRelationTable(id);
}
}
// clean the subtree record
accessSubTreeAlreadyWriteDBList = new Hashtable();
}
/* The method will compare all access modules in eml document -
* topLevel, additionalLevel(data access) and referenced access module*/
private void compareAllAccessModules() throws SAXException
{
String guid = docid+"."+revision;
try {
guid = IdentifierManager.getInstance().getGUID(docid, Integer.valueOf(revision));
} catch (Exception e) {
logMetacat.warn("Eml200SAXHandler.compareAllAccessModules - we can't get object identifier for metacat id "+guid);
}
//compare top level
compareAccessSubtree(topAccessSubTreeFromDB, topAccessSection, guid);
//compare additional level
int oldSize = additionalAccessSubTreeListFromDB.size();
int newSize = additionalAccessVector.size();
// if size is different, use deleted or added rules, so throw a exception
if (oldSize != newSize)
{
throw new SAXException(UPDATEACCESSERROR+guid);
}
//because access modules are both ordered in ASC in vectors, so we can
// compare one bye one
for ( int i = 0; i < newSize; i++)
{
AccessSection fromDB = (AccessSection)
additionalAccessSubTreeListFromDB.elementAt(i);
AccessSection fromParser = (AccessSection)
additionalAccessVector.elementAt(i);
compareAccessSubtree(fromDB, fromParser, guid);
}
//compare referenced level
Enumeration em = referencedAccessSubTreeListFromDB.keys();
while (em.hasMoreElements())
{
String id = (String)em.nextElement();
AccessSection fromDB = (AccessSection)
referencedAccessSubTreeListFromDB.get(id);
AccessSection fromParser = (AccessSection)
possibleReferencedAccessHash.get(id);
compareAccessSubtree(fromDB, fromParser, guid);
}
}
/* The method will compare two access subtree. Currently they compare to
* nodes one by one. It also can be changed to parse the node first, then
* compare the parsed result
*/
private void compareAccessSubtree(AccessSection fromDBTable,
AccessSection fromParser, String identifier)
throws SAXException
{
if (fromDBTable == null || fromParser == null)
{
throw new SAXException(UPDATEACCESSERROR+identifier);
}
Stack nodeStackFromDBTable = fromDBTable.getSubTreeNodeStack();
Stack nodeStackFromParser = fromParser.getStoredTmpNodeStack();
Stack tempStack = new Stack();
while(!nodeStackFromDBTable.isEmpty()){
tempStack.push(nodeStackFromDBTable.pop());
}
comparingNodeStacks(tempStack, nodeStackFromParser, identifier);
}
/* Compare two node stacks to see if they are same */
private void comparingNodeStacks(Stack stack1, Stack stack2, String identifier)
throws SAXException
{
// make sure stack1 and stack2 are not empty
if (stack1.isEmpty() || stack2.isEmpty()) {
logMetacat.info("Because stack is empty!");
throw new SAXException(UPDATEACCESSERROR+identifier);
}
// go throw two stacks and compare every element
while (!stack1.isEmpty()) {
// Pop an element from stack1
NodeRecord record1 = (NodeRecord) stack1.pop();
// Pop an element from stack2(stack 2 maybe empty)
NodeRecord record2 = null;
try {
record2 = (NodeRecord) stack2.pop();
} catch (EmptyStackException ee) {
logMetacat.error(
"Node stack2 is empty but stack1 isn't!");
throw new SAXException(UPDATEACCESSERROR+identifier);
}
// if two records are not same throw a exception
if (!record1.contentEquals(record2)) {
logMetacat.info("Two records from new and old stack are not "
+ "same!" + record1 + "--" +record2);
throw new SAXException(UPDATEACCESSERROR+identifier);
}//if
}//while
// now stack1 is empty and we should make sure stack2 is empty too
if (!stack2.isEmpty()) {
logMetacat.info(
"stack2 still have some elements while stack1 "
+ "is empty! ");
throw new SAXException(UPDATEACCESSERROR+identifier);
}//if
}//comparingNodeStacks
/* The method to write all access rule into db */
private void writeAccessRuleToDB() throws SAXException
{
// delete xml_accesssubtree table record for this docid
deleteAccessSubTreeRecord(docid);
//write additional access rule, and old records in xml_access will be
//deleted too
//System.out.println("before write additional access rules");
writeadditionalAccessRuleToDB();
//System.out.println("after write additional access rules");
//write top leve access rule, and old records in xml_access will be
//deleted too
if (topAccessSection != null){
writeTopLevelAccessRuleToDB();
}
//System.out.println("after write top access rules");
}//writeAccessRuleToDB
/* The method will figure out access reference for given access section -
* return a new AccessSection which contain access rules that be referenced.
* And will write the access subtree into xml_access table.
* this is a recursive method
*/
private AccessSection resolveAccessRuleReference(AccessSection access)
throws SAXException
{
if (access == null)
{
logMetacat.info("access module is null in " +
"resolveAccessRulesReference");
throw new SAXException("An access modules is null");
}
String subTreeId = access.getSubTreeId();
if (subTreeId == null ||
(subTreeId != null && !accessSubTreeAlreadyWriteDBList.contains(subTreeId)))
{
// we should record this access subtree into accesssubtree table.
// subtreeId is null means it can't be referenced. So this tree couldn't
// be stored twise in the table. Subtree is not null, but it is in
// hash yet, so it is new one.
writeAccessSubTreeIntoDB(access);
if (subTreeId != null)
{
accessSubTreeAlreadyWriteDBList.put(subTreeId, subTreeId);
}
}
String reference = access.getReferences();
if (reference != null)
{
// find the reference in top level
String topSubtreeId = topAccessSection.getSubTreeId();
if (topSubtreeId != null && topSubtreeId.equals(reference))
{
return resolveAccessRuleReference(topAccessSection);
}
else
{
// search it the additional access
for ( int i = 0; i <additionalAccessVector.size(); i++)
{
AccessSection additionalAccess = (AccessSection)
additionalAccessVector.elementAt(i);
String additionId = additionalAccess.getSubTreeId();
if (additionId != null && additionId.equals(reference))
{
return resolveAccessRuleReference(additionalAccess);
}// if
}// for
// search possible referenced access hashtable
if (possibleReferencedAccessHash.containsKey(reference))
{
AccessSection referenceAccess = (AccessSection)
possibleReferencedAccessHash.get(reference);
return resolveAccessRuleReference(referenceAccess);
}
// if hit here, this means you don't find any id match the reference
// throw a exception
throw new SAXException("No access module's id match the reference id");
}
}
else
{
// base line reference == null
AccessSection newAccessSection = new AccessSection();
access.copyPermOrderAndAccessRules(newAccessSection);
return newAccessSection;
}
}//resolveAccessRuleReference
/* This method will return a id which points a real distribution block if
* given a distribution id which is a reference. If the given id is a real
* distribution the id itself will be returned.
* Here is segment of eml
* <distribution id ="100"><online><url>abc</url></online></distribution>
* <distribution id ="200"><reference>100</reference></distribution>
* if the given value is 200, 100 will be returned.
* if the given value is 100, 100 will be returned.
*/
private String resolveDistributionReference(String givenId)
{
if (givenId == null )
{
return null;
}
if (!distributionReferenceList.containsKey(givenId))
{
//this is not reference distribution block, return given id
return givenId;
}
else
{
String referencedId = (String) distributionReferenceList.get(givenId);
// search util the referenced id is not in dsitribtionReferenceList
while (distributionReferenceList.containsKey(referencedId))
{
referencedId = (String) distributionReferenceList.get(referencedId);
}
return referencedId;
}
}
/* The method to write additional access rule into db. The old rules will be
* deleted
* If no describedId in the access object, this access rules will be ingorned
*/
private void writeadditionalAccessRuleToDB() throws SAXException
{
//System.out.println("in write additional");
// we should delete all inline access rules in xml_access if
// user has all permission
if (!needToCheckAccessModule)
{
deleteAllInlineDataAccessRules();
}
for (int i=0; i < additionalAccessVector.size(); i++)
{
//System.out.println("in for loop of write additional");
AccessSection access = (AccessSection)additionalAccessVector.elementAt(i);
Vector describeIdList = access.getDescribedIdList();
// if this access is a reference, a new access object will be created
// which contains the real access rules referenced. Also, each access tree
// will be write into xml_accesssubtee table
AccessSection newAccess = resolveAccessRuleReference(access);
String permOrder = newAccess.getPermissionOrder();
if (permOrder.equals(AccessControlInterface.DENYFIRST) && ignoreDenyFirst) {
logMetacat.warn("Metacat no longer supports EML 'denyFirst' access rules - ignoring this access block");
return;
}
Vector accessRule = newAccess.getAccessRules();
if (describeIdList == null || describeIdList.isEmpty())
{
continue;
}
for (int j = 0; j < describeIdList.size(); j++)
{
String subreeid = (String)describeIdList.elementAt(j);
logMetacat.info("describe id in additional access " +
subreeid);
// we need to figure out the real id if this subreeid is points to
// a distribution reference.
subreeid = resolveDistributionReference(subreeid);
if (subreeid != null && !subreeid.trim().equals(""))
{
logMetacat.info("subtree id is "+ subreeid +
" after resolve reference id" );
// if this id is for line data, we need to delete the records first
// then add new records. The key for deleting is subtee id
if (inlineDistributionIdList.containsKey(subreeid))
{
String inlineFileName = (String)
inlineDistributionIdList.get(subreeid);
deleteSubtreeAccessRule(subreeid);
logMetacat.info("Write inline data access into " +
"xml_access table for"+ inlineFileName);
writeGivenAccessRuleIntoDB(permOrder, accessRule,
inlineFileName, subreeid);
// Save guid of data object for syncing of access policy with CN after parsing
// is successful (see DocumentImpl.write)
// look-up pid assuming docid
String dataGuid = inlineFileName;
try {
String dataDocid = DocumentUtil.getDocIdFromAccessionNumber(inlineFileName);
int dataRev = DocumentUtil.getRevisionFromAccessionNumber(inlineFileName);
dataGuid = IdentifierManager.getInstance().getGUID(dataDocid, dataRev);
} catch (McdbDocNotFoundException e) {
// log the warning
logMetacat.warn("No pid found for [assumed] data docid: " + inlineFileName);
}
guidsToSync.add(dataGuid);
}
else if (onlineURLDistributionIdList.containsKey(subreeid))
{
String url = (String)onlineURLDistributionIdList.get(subreeid);
//this method will extrace data file id from url. It also will
// check if user can change the access rules for the data file id.
// if couldn't, it will throw a exception. Morover, the docid will
// be to relation id vector too.
// for online data, the subtree id we set is null.
// So in xml_access, only the inline data subteeid is not null
String dataFileName = handleOnlineUrlDataFile(url);
logMetacat.info("The data fileName in online url " +
dataFileName);
if (dataFileName != null)
{
deletePermissionsInAccessTableForDoc(dataFileName);
writeGivenAccessRuleIntoDB(permOrder, accessRule,
dataFileName, null);
logMetacat.info("Write online data access into " +
"xml_access table for " + dataFileName);
// Save guid of data object for syncing of access policy with CN after parsing
// is successful (see DocumentImpl.write)
// look-up pid assuming docid
String dataGuid = dataFileName;
try {
String dataDocid = DocumentUtil.getDocIdFromAccessionNumber(dataFileName);
int dataRev = DocumentUtil.getRevisionFromAccessionNumber(dataFileName);
dataGuid = IdentifierManager.getInstance().getGUID(dataDocid, dataRev);
} catch (McdbDocNotFoundException e) {
// log the warning
logMetacat.warn("No pid found for [assumed] data docid: " + dataFileName);
}
guidsToSync.add(dataGuid);
// put the id into a hashtalbe. So when we run wirtetop level
// access, those id will be ignored because they already has
// additional access rules
onlineURLIdHasadditionalAccess.put(subreeid, subreeid);
}
}//elseif
}//if
}//for
}//for
}//writeAdditonalLevelAccessRuletoDB
/* The method to write additional access rule into db. */
private void writeTopLevelAccessRuleToDB() throws SAXException
{
// if top access is reference, we need figure out the real access rules
// it points to
//System.out.println("permorder in top level" + topAccessSection.getPermissionOrder());
AccessSection newAccess = resolveAccessRuleReference(topAccessSection);
//System.out.println("permorder in new level" + newAccess.getPermissionOrder());
String permOrder = newAccess.getPermissionOrder();
if (permOrder.equals(AccessControlInterface.DENYFIRST) && ignoreDenyFirst) {
logMetacat.warn("Metacat no longer supports EML 'denyFirst' access rules - ignoring this access block");
return;
}
Vector accessRule = newAccess.getAccessRules();
String subtree = null;
// document itself
// use GUID
String guid = null;
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);
}
deletePermissionsInAccessTableForDoc(guid);
writeGivenAccessRuleIntoDB(permOrder, accessRule, guid, subtree);
// for online data, it includes with id and without id.
// 1. for the data with subtree id, we should ignore the ones already in
// the hash - onlineURLIdHasAddionalAccess.
// 2. for those without subreeid, it couldn't have additional access and we
// couldn't ignore it.
// 3. for inline data, we need do nothing because if it doesn't have
// additional access, it default value is the top one.
// here is the online url with id
Enumeration em = onlineURLDistributionIdList.keys();
while (em.hasMoreElements())
{
String onlineSubtreeId = (String)em.nextElement();
if (!onlineURLIdHasadditionalAccess.containsKey(onlineSubtreeId))
{
String url =
(String)onlineURLDistributionIdList.get(onlineSubtreeId);
String onlineDataId = handleOnlineUrlDataFile(url);
if (onlineDataId != null)
{
deletePermissionsInAccessTableForDoc(onlineDataId);
writeGivenAccessRuleIntoDB(permOrder, accessRule,
onlineDataId, subtree);
}
}
}//while
// here is the onlineURL without id
for (int i= 0; i < onlineURLDistributionListWithoutId.size(); i++)
{
String url = (String)onlineURLDistributionListWithoutId.elementAt(i);
String onlineDataId = handleOnlineUrlDataFile(url);
if (onlineDataId != null)
{
deletePermissionsInAccessTableForDoc(onlineDataId);
writeGivenAccessRuleIntoDB(permOrder, accessRule,
onlineDataId, subtree);
}
}//for
}//writeTopAccessRuletoDB
/* Write a gaven access rule into db */
private void writeGivenAccessRuleIntoDB(String permOrder, Vector accessRules,
String dataId, String subTreeId) throws SAXException
{
if (permOrder == null || permOrder.trim().equals("") || dataId == null ||
dataId.trim().equals("") || accessRules == null ||
accessRules.isEmpty())
{
logMetacat.info("The access object is null and tried to " +
" write to xml_access table");
throw new SAXException("The access object is null");
}
// geet the guid, not the docid alone
String guid = null;
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);
}
String sql = null;
PreparedStatement pstmt = null;
sql = "INSERT INTO xml_access (guid, principal_name, permission, "
+ "perm_type, perm_order, accessfileid, subtreeid) VALUES "
+ " (?, ?, ?, ?, ?, ?, ?)";
try
{
pstmt = connection.prepareStatement(sql);
// Increase DBConnection usage count
connection.increaseUsageCount(1);
// Bind the values to the query
pstmt.setString(1, dataId);
logMetacat.info("guid in accesstable: " + dataId);
pstmt.setString(6, guid);
logMetacat.info("Accessfileid in accesstable: " + guid);
pstmt.setString(5, permOrder);
logMetacat.info("PermOder in accesstable: " + permOrder);
pstmt.setString(7, subTreeId);
logMetacat.info("subtree id in accesstable: " + subTreeId);
// if it is not top level, set s id
//Vector accessRules = accessSection.getAccessRules();
// go through every rule
for (int i = 0; i < accessRules.size(); i++)
{
AccessRule rule = (AccessRule) accessRules.elementAt(i);
String permType = rule.getPermissionType();
int permission = rule.getPermission();
pstmt.setInt(3, permission);
logMetacat.info("permission in accesstable: "
+ permission);
pstmt.setString(4, permType);
logMetacat.info(
"Permtype in accesstable: " + permType);
// go through every principle in rule
Vector nameVector = rule.getPrincipal();
for (int j = 0; j < nameVector.size(); j++)
{
String prName = (String) nameVector.elementAt(j);
pstmt.setString(2, prName);
logMetacat.info("Principal in accesstable: "
+ prName);
logMetacat.debug("running sql: " + pstmt.toString());
pstmt.execute();
}//for
}//for
pstmt.close();
}//try
catch (SQLException e)
{
throw new SAXException("EMLSAXHandler.writeAccessRuletoDB(): "
+ e.getMessage());
}//catch
finally
{
try
{
pstmt.close();
}
catch (SQLException ee)
{
throw new SAXException("EMLSAXHandler.writeAccessRuletoDB(): "
+ ee.getMessage());
}
}//finally
// for D1, refresh the entries
HazelcastService.getInstance().refreshSystemMetadataEntry(guid);
HazelcastService.getInstance().refreshSystemMetadataEntry(dataId);
}//writeGivenAccessRuleIntoDB
/* Delete from db all permission for resources related guid, if any. */
private void deletePermissionsInAccessTableForDoc(String guid)
throws SAXException
{
PreparedStatement pstmt = null;
try {
String sql = "DELETE FROM xml_access WHERE guid = ? ";
// delete all acl records for resources related to guid if any
pstmt = connection.prepareStatement(sql);
pstmt.setString(1, guid);
// Increase DBConnection usage count
connection.increaseUsageCount(1);
pstmt.execute();
} catch (SQLException e) {
throw new SAXException(e.getMessage());
} finally {
try {
pstmt.close();
} catch (SQLException ee) {
throw new SAXException(ee.getMessage());
}
}
}//deletePermissionsInAccessTable
/* Delete access rules from xml_access for a subtee id */
private void deleteSubtreeAccessRule(String subtreeid) throws SAXException
{
PreparedStatement pstmt = null;
try
{
String sql =
"DELETE FROM xml_access " +
"WHERE accessfileid IN (SELECT guid from identifier where docid = ? and rev = ?) " +
"AND subtreeid = ?";
pstmt = connection.prepareStatement(sql);
pstmt.setString(1, docid);
pstmt.setInt(2, Integer.valueOf(revision));
pstmt.setString(3, subtreeid);
// Increase DBConnection usage count
connection.increaseUsageCount(1);
pstmt.execute();
}
catch (SQLException e)
{
throw new SAXException(e.getMessage());
}
finally
{
try
{
pstmt.close();
}
catch (SQLException ee)
{
throw new SAXException(ee.getMessage());
}
}
}
private void deleteAllInlineDataAccessRules() throws SAXException
{
PreparedStatement pstmt = null;
try
{
String sql =
"DELETE FROM xml_access " +
"WHERE accessfileid IN (SELECT guid from identifier where docid = ? and rev = ?) " +
"AND subtreeid IS NOT NULL";
pstmt = connection.prepareStatement(sql);
pstmt.setString(1, docid);
pstmt.setInt(2, Integer.valueOf(revision));
// Increase DBConnection usage count
connection.increaseUsageCount(1);
pstmt.execute();
}
catch (SQLException e)
{
throw new SAXException(e.getMessage());
}
finally
{
try
{
pstmt.close();
}
catch (SQLException ee)
{
throw new SAXException(ee.getMessage());
}
}
}
/*
* 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)
throws SAXException
{
if (accessSection == null)
{
logMetacat.info("Access object is null and tried to write "+
"into access subtree table");
throw new SAXException("The access object is null to write access " +
"sbutree");
}
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);
String level = accessSection.getControlLevel();
long startNodeId = -1;
if (level != null && level.equals(DATAACCESSLEVEL))
{
// for additional access module the start node id should be
// descirbes element id
startNodeId = accessSection.getStartedDescribesNodeId();
// if in additional access, there is not describes element,
// in this senario, describesNodeId will be -1. Then we should
// the start access element id
if (startNodeId == -1)
{
startNodeId = accessSection.getStartNodeId();
}
}
else
{
startNodeId = accessSection.getStartNodeId();
}
long endNodeId = accessSection.getEndNodeId();
String sectionId = accessSection.getSubTreeId();
if (startNodeId ==-1 || endNodeId == -1)
{
throw new SAXException("Don't find start node or end node id " +
"for the access subtee");
}
// Bind the values to the query
pstmt.setString(1, docid);
logMetacat.info("Docid in access-subtreetable: " + docid);
pstmt.setInt(2, (new Integer(revision)).intValue());
logMetacat.info("rev in accesssubtreetable: " + revision);
pstmt.setString(3, level);
logMetacat.info("contorl level in access-subtree table: "
+ level);
pstmt.setString(4, sectionId);
logMetacat.info("Subtree id in access-subtree table: "
+ sectionId);
pstmt.setLong(5, startNodeId);
logMetacat.info("Start node id is: " + startNodeId);
pstmt.setLong(6, endNodeId);
logMetacat.info("End node id is: " + endNodeId);
logMetacat.trace("Eml200SAXHandler.writeAccessSubTreeIntoDB - executing 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
{
PreparedStatement pstmt = null;
try {
String sql = "DELETE FROM xml_accesssubtree WHERE docid = ?";
// delete all acl records for resources related to @aclid if any
pstmt = connection.prepareStatement(sql);
pstmt.setString(1, docId);
// Increase DBConnection usage count
connection.increaseUsageCount(1);
logMetacat.debug("running sql: " + sql);
pstmt.execute();
} catch (SQLException e) {
throw new SAXException(e.getMessage());
} finally {
try {
pstmt.close();
} catch (SQLException ee) {
throw new SAXException(ee.getMessage());
}
}
}//deleteAccessSubTreeRecord
// open a file writer for writing inline data to file
private Writer createInlineDataFileWriter(String fileName, String encoding)
throws SAXException
{
Writer writer = null;
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.info("inline file name: " + newFile);
try {
// true means append
writer = new OutputStreamWriter(new FileOutputStream(newFile, true), encoding);
} catch (IOException ioe) {
throw new SAXException(ioe.getMessage());
}
return writer;
}
// write inline data into file system and return file name(without path)
private void writeInlineDataIntoFile(Writer writer, StringBuffer data)
throws SAXException
{
try {
writer.write(data.toString());
writer.flush();
} catch (Exception e) {
throw new SAXException(e.getMessage());
}
}
/*
* In eml2, the inline data wouldn't store in db, it store in file system
* The db stores file name(without path). We got the old file name from db
* and compare to the new in line data file
*/
public boolean compareInlineDataFiles(String oldFileName, String newFileName)
throws McdbException
{
// this method need to be testing
boolean same = true;
String data = null;
try {
String path = PropertyService.getProperty("application.inlinedatafilepath");
// the new file name will look like path/docid.rev.2
File inlineDataDirectory = new File(path);
File oldDataFile = new File(inlineDataDirectory, oldFileName);
File newDataFile = new File(inlineDataDirectory, newFileName);
Reader oldFileReader = new InputStreamReader(new FileInputStream(oldDataFile), encoding);
BufferedReader oldStringReader = new BufferedReader(oldFileReader);
Reader newFileReader = new InputStreamReader(new FileInputStream(newDataFile), encoding);
BufferedReader newStringReader = new BufferedReader(newFileReader);
// read first line of data
String oldString = oldStringReader.readLine();
String newString = newStringReader.readLine();
// at the end oldstring will be null
while (oldString != null) {
oldString = oldStringReader.readLine();
newString = newStringReader.readLine();
if (!oldString.equals(newString)) {
same = false;
break;
}
}
// if oldString is null but newString is not null, they are same
if (same) {
if (newString != null) {
same = false;
}
}
} catch (Exception e) {
throw new McdbException(e.getMessage());
}
logMetacat.info("the inline data retrieve from file: " + data);
return same;
}
/*
* Copy a old line file to a new inline file
*/
public void copyInlineFile(String inlineDistributionId, String newFileName)
throws SAXException {
if (inlineDistributionId == null || newFileName == null) {
throw new SAXException("Could not copy inline file from old one to new "
+ "one!");
}
// get old file id from previousUnreadable data object
String oldInlineInternalFileName = (String) previousUnreadableInlineDataObjectHash
.get(inlineDistributionId);
if (oldInlineInternalFileName == null
|| oldInlineInternalFileName.trim().equals("")) {
throw new SAXException("Could not copy inline file from old one to new "
+ "one because can't find old file name");
}
logMetacat.info("in handle inline data");
logMetacat.info("the inline data file name from xml_access is: "
+ oldInlineInternalFileName);
InputStream oldFileReader = null;
OutputStream newFileWriter = null;
try {
String path = PropertyService.getProperty("application.inlinedatafilepath");
// the new file name will look like path/docid.rev.2
File inlineDataDirectory = new File(path);
File oldDataFile = new File(inlineDataDirectory, oldInlineInternalFileName);
File newDataFile = new File(inlineDataDirectory, newFileName);
oldFileReader = new FileInputStream(oldDataFile);
newFileWriter = new FileOutputStream(newDataFile);
byte[] buf = new byte[4 * 1024]; // 4K buffer
int b = oldFileReader.read(buf);
while (b != -1) {
newFileWriter.write(buf, 0, b);
b = oldFileReader.read(buf);
}
} catch (Exception e) {
throw new SAXException(e.getMessage());
} finally {
if (oldFileReader != null) {
try {
oldFileReader.close();
} catch (Exception ee) {
throw new SAXException(ee.getMessage());
}
}
if (newFileWriter != null) {
try {
newFileWriter.close();
} catch (Exception ee) {
throw new SAXException(ee.getMessage());
}
}
}
}
// 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 = (String) inlineFileIDList.elementAt(i);
deleteInlineDataFile(fileName);
}
}
}
/* 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();
}
/*
* In eml2, the inline data wouldn't store in db, it store in file system
* The db stores file name(without path).
*/
public static Reader readInlineDataFromFileSystem(String fileName, String encoding)
throws McdbException {
// BufferedReader stringReader = null;
Reader fileReader = null;
try {
String path = PropertyService.getProperty("application.inlinedatafilepath");
// the new file name will look like path/docid.rev.2
File inlineDataDirectory = new File(path);
File dataFile = new File(inlineDataDirectory, fileName);
fileReader = new InputStreamReader(new FileInputStream(dataFile), encoding);
// stringReader = new BufferedReader(fileReader);
} catch (Exception e) {
throw new McdbException(e.getMessage());
}
// return stringReader;
return fileReader;
}
/* 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
logMetacat.trace("Eml200SAXHandler.deleteRelations - executing SQL: " + pStmt.toString());
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
}
/* 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);
pStmt.setString(2, doctype);
pStmt.setString(3, docid);
pStmt.setString(4, RELATION);
pStmt.setString(5, dataId);
//execute query
logMetacat.trace("Eml200SAXHandler.writeOnlineDataFileIdIntoRelationTable - executing SQL: " + pStmt.toString());
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
}//writeOnlineDataFileIdIntoRelationTable
/*
* This method will handle data file in online url. If the data file is in
* ecogrid protocol, then the datafile identifier (guid) be returned.
* otherwise, null will be returned.
* 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 (guid) will be returned
* 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 String handleOnlineUrlDataFile(String url) throws SAXException
{
logMetacat.warn("The url is "+ url);
String docid = null;
String guid = null;
// if the url is not a ecogrid protocol, null will be getten
String accessionNumber =
DocumentUtil.getAccessionNumberFromEcogridIdentifier(url);
// check for valid docid.rev
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;
}
}
if (accessionNumber != null)
{
try {
guid = IdentifierManager.getInstance().getGUID(docid, rev);
} catch (McdbDocNotFoundException e1) {
guid = docid + "." + rev;
IdentifierManager.getInstance().createMapping(guid, guid);
}
onlineDataFileIdInRelationVector.add(docid);
try
{
if (!AccessionNumber.accNumberUsed(docid))
{
return guid;
}
// 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;
PermissionController controller = new PermissionController(previousDocid);
if(writeAccessRules) {
if (controller.hasPermission(user, groups, AccessControlInterface.ALLSTRING)
|| controller.hasPermission(user, groups, AccessControlInterface.CHMODSTRING)) {
return guid;
}
else
{
throw new SAXException("User: " + user + " does not have permission to update " +
"access rules for data file "+ guid);
}
}
}//try
catch(Exception e)
{
logMetacat.error("Error in " +
"Eml200SAXHanlder.handleOnlineUrlDataFile is " +
e.getMessage());
throw new SAXException(e.getMessage());
}
}
return guid;
}
private void compareElementNameSpaceAttributes(Stack unchangableNodeStack,
Hashtable nameSpaces, Attributes attributes, String localName,
String error) throws SAXException
{
//Get element subtree node stack (element node)
NodeRecord elementNode = null;
try {
elementNode = (NodeRecord) unchangableNodeStack.pop();
} catch (EmptyStackException ee) {
logMetacat.error("Node stack is empty for element data");
throw new SAXException(error);
}
logMetacat.info("current node type from xml is ELEMENT");
logMetacat.info("node type from stack: "
+ elementNode.getNodeType());
logMetacat.info("node name from xml document: " + localName);
logMetacat.info("node name from stack: "
+ elementNode.getNodeName());
logMetacat.info("node data from stack: "
+ elementNode.getNodeData());
logMetacat.info("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.info("Inconsistence happend: ");
logMetacat.info("current node type from xml is ELEMENT");
logMetacat.info("node type from stack: "
+ elementNode.getNodeType());
logMetacat.info("node name from xml document: "
+ localName);
logMetacat.info("node name from stack: "
+ elementNode.getNodeName());
logMetacat.info("node data from stack: "
+ elementNode.getNodeData());
logMetacat.info("node id is: " + elementNode.getNodeId());
throw new SAXException(error);
}
//compare namespace
Enumeration nameEn = nameSpaces.keys();
while (nameEn.hasMoreElements()) {
//Get namespacke node stack (element node)
NodeRecord nameNode = null;
try {
nameNode = (NodeRecord) unchangableNodeStack.pop();
} catch (EmptyStackException ee) {
logMetacat.error(
"Node stack is empty for namespace data");
throw new SAXException(error);
}
String prefixName = (String) nameEn.nextElement();
String nameSpaceUri = (String) nameSpaces.get(prefixName);
if (!nameNode.getNodeType().equals("NAMESPACE")
|| !prefixName.equals(nameNode.getNodeName())
|| !nameSpaceUri.equals(nameNode.getNodeData())) {
logMetacat.info("Inconsistence happend: ");
logMetacat.info(
"current node type from xml is NAMESPACE");
logMetacat.info("node type from stack: "
+ nameNode.getNodeType());
logMetacat.info("current node name from xml is: "
+ prefixName);
logMetacat.info("node name from stack: "
+ nameNode.getNodeName());
logMetacat.info("current node data from xml is: "
+ nameSpaceUri);
logMetacat.info("node data from stack: "
+ nameNode.getNodeData());
logMetacat.info("node id is: " + nameNode.getNodeId());
throw new SAXException(error);
}
}//while
//compare attributes
for (int i = 0; i < attributes.getLength(); i++) {
NodeRecord attriNode = null;
try {
attriNode = (NodeRecord) unchangableNodeStack.pop();
} 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.info(
"current node type from xml is ATTRIBUTE ");
logMetacat.info("node type from stack: "
+ attriNode.getNodeType());
logMetacat.info("current node name from xml is: "
+ attributeName);
logMetacat.info("node name from stack: "
+ attriNode.getNodeName());
logMetacat.info("current node data from xml is: "
+ attributeValue);
logMetacat.info("node data from stack: "
+ attriNode.getNodeData());
logMetacat.info("node id is: " + attriNode.getNodeId());
if (!attriNode.getNodeType().equals("ATTRIBUTE")
|| !attributeName.equals(attriNode.getNodeName())
|| !attributeValue.equals(attriNode.getNodeData())) {
logMetacat.info("Inconsistence happend: ");
logMetacat.info(
"current node type from xml is ATTRIBUTE ");
logMetacat.info("node type from stack: "
+ attriNode.getNodeType());
logMetacat.info("current node name from xml is: "
+ attributeName);
logMetacat.info("node name from stack: "
+ attriNode.getNodeName());
logMetacat.info("current node data from xml is: "
+ attributeValue);
logMetacat.info("node data from stack: "
+ attriNode.getNodeData());
logMetacat.info("node is: " + attriNode.getNodeId());
throw new SAXException(error);
}
}//for
}
/* mehtod to compare current text node and node in db */
private void compareTextNode(Stack nodeStack, StringBuffer text,
String error) throws SAXException
{
NodeRecord node = null;
//get node from current stack
try {
node = (NodeRecord) nodeStack.pop();
} catch (EmptyStackException ee) {
logMetacat.error(
"Node stack is empty for text data in startElement");
throw new SAXException(error);
}
logMetacat.info(
"current node type from xml is TEXT in start element");
logMetacat.info("node type from stack: " + node.getNodeType());
logMetacat.info("current node data from xml is: "
+ text.toString());
logMetacat.info("node data from stack: " + node.getNodeData());
logMetacat.info("node name from stack: " + node.getNodeName());
logMetacat.info("node is: " + node.getNodeId());
if (!node.getNodeType().equals("TEXT")
|| !(text.toString()).equals(node.getNodeData())) {
logMetacat.info("Inconsistence happend: ");
logMetacat.info(
"current node type from xml is TEXT in start element");
logMetacat.info("node type from stack: "
+ node.getNodeType());
logMetacat.info("current node data from xml is: "
+ text.toString());
logMetacat.info("node data from stack: "
+ node.getNodeData());
logMetacat.info("node name from stack: "
+ node.getNodeName());
logMetacat.info("node is: " + node.getNodeId());
throw new SAXException(error);
}//if
}
/* Comparet comment from xml and db */
private void compareCommentNode(Stack nodeStack, String string, String error)
throws SAXException
{
NodeRecord node = null;
try {
node = (NodeRecord) nodeStack.pop();
} catch (EmptyStackException ee) {
logMetacat.error("the stack is empty for comment data");
throw new SAXException(error);
}
logMetacat.info("current node type from xml is COMMENT");
logMetacat.info("node type from stack: " + node.getNodeType());
logMetacat.info("current node data from xml is: " + string);
logMetacat.info("node data from stack: " + node.getNodeData());
logMetacat.info("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.info("Inconsistence happend: ");
logMetacat.info("current node type from xml is COMMENT");
logMetacat.info("node type from stack: "
+ node.getNodeType());
logMetacat.info(
"current node data from xml is: " + string);
logMetacat.info("node data from stack: "
+ node.getNodeData());
logMetacat.info("node is from stack: " + node.getNodeId());
throw new SAXException(error);
}//if
}
/* Compare whitespace from xml and db */
private void compareWhiteSpace(Stack nodeStack, String string, String error)
throws SAXException
{
NodeRecord node = null;
try {
node = (NodeRecord) 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.info("Inconsistence happend: ");
logMetacat.info(
"current node type from xml is WHITESPACE TEXT");
logMetacat.info("node type from stack: "
+ node.getNodeType());
logMetacat.info(
"current node data from xml is: " + string);
logMetacat.info("node data from stack: "
+ node.getNodeData());
logMetacat.info("node is from stack: " + node.getNodeId());
throw new SAXException(error);
}//if
}
}