Metacat

/**

 *  '$RCSfile$'

 *    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

 *    Release: @release@

 *

 *   '$Author$'

 *     '$Date$'

 * '$Revision$'

 *

 * This program is free software; you can redistribute it and/or modify

 * it under the terms of the GNU General Public License as published by

 * the Free Software Foundation; either version 2 of the License, or

 * (at your option) any later version.

 *

 * This program is distributed in the hope that it will be useful,

 * but WITHOUT ANY WARRANTY; without even the implied warranty of

 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 * GNU General Public License for more details.

 *

 * You should have received a copy of the GNU General Public License

 * along with this program; if not, write to the Free Software

 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

 */

package edu.ucsb.nceas.metacat;

import java.io.BufferedReader;

import java.io.File;

import java.io.FileReader;

import java.io.FileWriter;

import java.io.IOException;

import java.io.Reader;

import java.sql.PreparedStatement;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.sql.Statement;

import java.util.EmptyStackException;

import java.util.Enumeration;

import java.util.Hashtable;

import java.util.Stack;

import java.util.Vector;

import org.xml.sax.Attributes;

import org.xml.sax.SAXException;

/**

 * A database aware Class implementing callback bethods for the SAX parser to

 * call when processing the XML stream and generating events

 */

public class Eml210SAXHandler extends DBSAXHandler implements

        AccessControlInterface

{

    private Vector allowRules = new Vector();

    private Vector denyRules = new Vector();

    private String documentId = null;

    private Vector subDocumentIdList = new Vector();

    private boolean processTopLeverAccess = false;

    private boolean processAdditionalAccess = false;

    private boolean processOtherAccess = false;

    private AccessSection accessObject = null;

    private AccessRule accessRule = null;

    private Vector accessObjectList = new Vector(); // store every access rule

    private Hashtable topLevelAccessControlMap = new Hashtable();

    private Hashtable additionalAccessControlMap = new Hashtable();// store

    //subtree access for single

    // additionalmetacat

    private Vector additionalAccessMapList = new Vector();// store maps for

    // every addionalmetadata

    private Vector describesId = new Vector(); // store the ids in

    //additionalmetadata/describes

    private Stack subTreeInfoStack = new Stack();

    private Vector subTreeList = new Vector();// store the final subtree

    private Hashtable unChangableSubTreeHash = new Hashtable();

    private Stack currentUnChangedableSubtreeNodeStack = new Stack();

    private boolean startCriticalSubTree = false;

    private boolean firstElementForCriticalSubTree = false;

    private String firstElementNameForCriticalSubTree;

    private boolean needCheckingAccessModule = false;

    private Vector unChangableAccessSubTreeVector = new Vector();

    private Stack currentUnchangableAccessModuleNodeStack = new Stack();

    private AccessSection topAccessSection;

    // 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();

    // vector stored the data file id which will be write top access rules to

   // access table

    private Vector onlineDataFileIdInTopAccessVector = new Vector();

    // Indicator of inline data

    private boolean handleInlineData = false;

    private Stack inlineDataNodeStack = null;

    private Hashtable inlineDataNameSpace = null;

    private FileWriter inlineDataFileWriter = null;

    private String inlineDataFileName = null;

    private int inLineDataIndex = 0;

    private Vector inlineFileIDList = new Vector();

    // 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 URL = "url";

    private static final String PERMISSIONERROR = "User try to update a subtree"

            + " which it doesn't have write permission!";

    private static final String UPDATEACCESSERROR = "User try to update a "

            + "access module which it doesn't have \"ALL\" permission!";

    private static final String TOPLEVEL = "top";

    private static final String SUBTREELEVEL = "subtree";

    private static final String RELATION = "Provides info for";

    /**

     * 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 Eml210SAXHandler(DBConnection conn, String action, String docid,

            String revision, String user, String[] groups, String pub,

            int serverCode) throws SAXException

    {

        super(conn, action, docid, revision, user, groups, pub, serverCode);

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

        try {

            PermissionController control = new PermissionController(docid

                    + MetaCatUtil.getOption("accNumSeparator") + revision);

            //unChangableSubTreeHash = getUnchangableSubTree(control, user,

            // groups);

            //If the action is update and user doesn't have "ALL" permission

            // we need to check if user update access subtree

            if (action.equals("UPDATE")

                    && !control.hasPermission(user, groups,

                            AccessControlInterface.ALLSTRING)) {

                needCheckingAccessModule = true;

                unChangableAccessSubTreeVector = getAccessSubTreeListFromDB();

            }

        } catch (Exception e) {

            throw new SAXException(e.getMessage());

        }

    }

    /* Pass a permission control and get the list of unchangable subtree */

    private Hashtable getUnchangableSubTree(PermissionController controller,

            String user, String[] groups) throws Exception

    {

        Hashtable list = null;

        Hashtable result = new Hashtable();

        // get unwritable sutree from controller

        // changed after old code removal

        //controller.hasUnaccessableSubTree(user, groups,

        //        AccessControlInterface.WRITESTRING);

            Enumeration en = list.elements();

            while (en.hasMoreElements()) {

                // Get a subtree without node record list

                SubTree treeWithoutStack = (SubTree) en.nextElement();

                String subTreeId = treeWithoutStack.getSubTreeId();

                MetaCatUtil.debugMessage(

                        "unchangable subtree id: " + subTreeId, 40);

                long startNodeId = treeWithoutStack.getStartNodeId();

                MetaCatUtil.debugMessage("unchangable subtree startnodeid: "

                        + startNodeId, 40);

                long endNodeId = treeWithoutStack.getEndNodeId();

                MetaCatUtil.debugMessage("unchangable subtree endnodeid: "

                        + endNodeId, 40);

                // Get a subtree has the nodelist

                SubTree tree = new SubTree(docid, subTreeId, startNodeId,

                        endNodeId);

                // add this tree to the result

                result.put(subTreeId, tree);

            }//while

        }//if

        return result;

    }

    /*

     * Get the subtree node info from xml_accesssubtree table

     */

    private Vector getAccessSubTreeListFromDB() throws Exception

    {

        Vector result = new Vector();

        PreparedStatement pstmt = null;

        ResultSet rs = null;

        String sql = "SELECT controllevel, subtreeid, startnodeid, endnodeid "

                + "FROM xml_accesssubtree WHERE docid 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.execute();

            // 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);

                // 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;

    }

    /** 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

        MetaCatUtil.debugMessage("Start ELEMENT(qName) " + qName, 50);

        MetaCatUtil.debugMessage("Start ELEMENT(localName) " + localName, 50);

        MetaCatUtil.debugMessage("Start ELEMENT(uri) " + uri, 50);

        DBSAXNode parentNode = null;

        DBSAXNode currentNode = null;

        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 (localName.equals(INLINE)) {

                handleInlineData = true;

                inLineDataIndex++;

                //intitialize namespace hash for in line data

                inlineDataNameSpace = new Hashtable();

                //initialize file writer

                String docidWithoutRev = MetaCatUtil.getDocIdFromString(docid);

                String seperator = MetaCatUtil.getOption("accNumSeparator");

                // the new file name will look like docid.rev.2

                inlineDataFileName = docidWithoutRev + seperator + revision

                        + seperator + inLineDataIndex;

                inlineDataFileWriter = createInlineDataFileWriter(inlineDataFileName);

                // put the inline file id into a vector. If upload failed,

                // metacat will

                // delete the inline data file

                inlineFileIDList.add(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) {

                //compare text node data for unchangesubtree

                if (startCriticalSubTree) {

                    compareTextNode(currentUnChangedableSubtreeNodeStack,

                            textBuffer, PERMISSIONERROR);

                }//if

                //compare top level access module

                if (processTopLeverAccess && needCheckingAccessModule) {

                    compareTextNode(currentUnchangableAccessModuleNodeStack,

                            textBuffer, UPDATEACCESSERROR);

                }

                if (needCheckingAccessModule

                        && (processAdditionalAccess || processOtherAccess || processTopLeverAccess)) {

                    // 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;

                    }

                    MetaCatUtil.debugMessage("DOCNAME-a: " + docname, 30);

                    MetaCatUtil.debugMessage("DOCTYPE-a: " + doctype, 30);

                } 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;

                    MetaCatUtil.debugMessage("DOCTYPE-b: " + doctype, 30);

                }

                rootNode.writeNodename(docname);

                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();

                        Statement stmt = dbConn.createStatement();

                        ResultSet rs = stmt

                                .executeQuery("SELECT catalog_id FROM xml_catalog "

                                        + "WHERE entry_type = 'Schema' "

                                        + "AND public_id = '" + doctype + "'");

                        boolean hasRow = rs.next();

                        if (hasRow) {

                            catalogid = rs.getString(1);

                        }

                        stmt.close();

                    }//try

                    finally {

                        // Return dbconnection

                        DBConnectionPool.returnDBConnection(dbConn,

                                serialNumber);

                    }//finally

                    //create documentImpl object by the constructor which can

                    // specify

                    //the revision

                    currentDocument = new DocumentImpl(connection, rootNode

                            .getNodeID(), docname, doctype, docid, revision,

                            action, user, this.pub, catalogid, this.serverCode);

                } catch (Exception ane) {

                    throw (new SAXException(

                            "Error in EMLSaxHandler.startElement " + action,

                            ane));

                }

            }

            // Create the current node representation

            currentNode = new DBSAXNode(connection, qName, localName,

                    parentNode, currentDocument.getRootNodeID(), docid,

                    currentDocument.getDoctype());

            // 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);

            }

            // 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)) {

                    //check unchangedable subtree hash if contains this

                    // subtree id

                    if (unChangableSubTreeHash.containsKey(attributeValue)) {

                        // this subtree couldn't be changed by the user and

                        // move it from hash

                        SubTree currentUnChangedableSubtree = (SubTree) unChangableSubTreeHash

                                .remove(attributeValue);

                        currentUnChangedableSubtreeNodeStack = currentUnChangedableSubtree

                                .getSubTreeNodeStack();

                        startCriticalSubTree = true;

                        firstElementForCriticalSubTree = true;

                    }

                    // handle subtree info

                    SubTree subTress = new SubTree();

                    // set sub tree id

                    subTress.setSubTreeId(attributeValue);

                    // set sub tree sstart lement name

                    subTress.setStartElementName(currentNode.getTagName());

                    // set start node number

                    subTress.setStartNodeId(startNodeId);

                    // add to stack, but it didn't get end node id yet

                    subTreeInfoStack.push(subTress);

                }

            }//for

            // handle access stuff

            if (localName.equals(ACCESS)) {

                // if it is in addtionalmetacat

                if (parentNode.getTagName() == ADDITIONALMETADATA) {

                    processAdditionalAccess = true;

                } else {

                    //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)) {

                        processTopLeverAccess = true;

                    } else {

                        // process other access embedded into resource level

                        // module

                        processOtherAccess = 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);

                accessObject.setStartNodeId(startNodeId);

                accessObject.setDocId(docid);

                // load top level node stack to

                // currentUnchangableAccessModuleNodeStack

                if (processTopLeverAccess && needCheckingAccessModule) {

                    // get the node stack for

                    currentUnchangableAccessModuleNodeStack = topAccessSection

                            .getSubTreeNodeStack();

                }

            }

            // 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);

            }

            // 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);

            // handle critical subtree

            if (startCriticalSubTree && firstElementForCriticalSubTree) {

                //store the element name

                firstElementNameForCriticalSubTree = qName;

                firstElementForCriticalSubTree = false;

            }//for first element

            // handle critical subtree

            if (startCriticalSubTree) {

                compareElementNameSpaceAttributes(

                        currentUnChangedableSubtreeNodeStack, namespaces, atts,

                        localName, PERMISSIONERROR);

            }

            //compare top access level module

            if (processTopLeverAccess && needCheckingAccessModule) {

                compareElementNameSpaceAttributes(

                        currentUnchangableAccessModuleNodeStack, namespaces,

                        atts, localName, UPDATEACCESSERROR);

            }

            // store access module element and attributes into stored stack

            if (needCheckingAccessModule

                    && (processAdditionalAccess || processOtherAccess || processTopLeverAccess)) {

                // 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);

                }

            }

            // reset name space

            namespaces = null;

            namespaces = new Hashtable();

        }//not 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) 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();

            //write inline data into file

            MetaCatUtil.debugMessage("the inline element data is: "

                    + inlineElements.toString(), 50);

            writeInlineDataIntoFile(inlineDataFileWriter, inlineElements);

        }//else

    }

    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) {

            MetaCatUtil

                    .debugMessage("Node stack is empty for element data", 35);

            throw new SAXException(error);

        }

        MetaCatUtil.debugMessage("current node type from xml is ELEMENT", 40);

        MetaCatUtil.debugMessage("node type from stack: "

                + elementNode.getNodeType(), 40);

        MetaCatUtil.debugMessage("node name from xml document: " + localName,

                40);

        MetaCatUtil.debugMessage("node name from stack: "

                + elementNode.getNodeName(), 40);

        MetaCatUtil.debugMessage("node data from stack: "

                + elementNode.getNodeData(), 40);

        MetaCatUtil.debugMessage("node id is: " + elementNode.getNodeId(), 40);

        // 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())))

        {

            MetaCatUtil.debugMessage("Inconsistence happend: ", 40);

            MetaCatUtil.debugMessage("current node type from xml is ELEMENT",

                    40);

            MetaCatUtil.debugMessage("node type from stack: "

                    + elementNode.getNodeType(), 40);

            MetaCatUtil.debugMessage("node name from xml document: "

                    + localName, 40);

            MetaCatUtil.debugMessage("node name from stack: "

                    + elementNode.getNodeName(), 40);

            MetaCatUtil.debugMessage("node data from stack: "

                    + elementNode.getNodeData(), 40);

            MetaCatUtil.debugMessage("node id is: " + elementNode.getNodeId(),

                    40);

            throw new SAXException(error);

        }

        //compare namespace

        Enumeration nameEn = nameSpaces.keys();

        while (nameEn.hasMoreElements()) {

            //Get namespacke node stack (element node)

            NodeRecord nameNode = null;