source: main/trunk/gli/src/org/greenstone/gatherer/metadata/MetadataXMLFile.java@ 33737

/**
 *############################################################################
 * A component of the Greenstone Librarian Interface, part of the Greenstone
 * digital library suite from the New Zealand Digital Library Project at the
 * University of Waikato, New Zealand.
 *
 * Author: Michael Dewsnip, NZDL Project, University of Waikato, NZ
 *
 * Copyright (C) 2004 New Zealand Digital Library Project
 *
 * 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., 675 Mass Ave, Cambridge, MA 02139, USA.
 *############################################################################
 */

package org.greenstone.gatherer.metadata;


import java.io.*;
import java.util.*;
import org.greenstone.gatherer.DebugStream;
import org.greenstone.gatherer.collection.CollectionTreeNode;
import org.greenstone.gatherer.util.XMLTools;
import org.w3c.dom.*;

import org.greenstone.gatherer.util.Utility;

/** This class represents one metadata.xml file */
public class MetadataXMLFile
    extends File
{
    static final private String DESCRIPTION_ELEMENT = "Description";
    static final private String DIRECTORY_FILENAME = ".*";
    static final private String FILENAME_ELEMENT = "FileName";
    static final private String FILESET_ELEMENT = "FileSet";
    static final private String METADATA_ELEMENT = "Metadata";
    static final private String[] nonEscapingElements = new String[]{FILENAME_ELEMENT};
    
    /** Special metadata field: the filename encoding is a unique sort of metadata in
     * that it is not just information stored with a collection file, but also needs to
     * be applied in real-time to the collection file (to its filename) for display. */
    static final public String FILENAME_ENCODING_METADATA = "gs.filenameEncoding";
    
    // To speed things up a bit we keep the last accessed metadata.xml file in memory
    static private File loaded_file = null;
    static private Document loaded_file_document = null;
    static private boolean loaded_file_changed = false;


    public MetadataXMLFile(String metadata_xml_file_path)
    {
    super(metadata_xml_file_path);
    }


    public void addMetadata(CollectionTreeNode file_node, ArrayList metadata_values)
    {
    // If this metadata.xml file isn't the one currently loaded, load it now
    if (loaded_file != this) {
        // First we must save out the currently loaded file
        saveLoadedFile();

        // Parse the metadata.xml file
        Document document = XMLTools.parseXMLFile(this);
            if (document == null) {
        System.err.println("Error: Could not parse metadata.xml file " + getAbsolutePath());
        return;
        }

        loaded_file = this;
        loaded_file_document = document;
        reEncodeFilenamesInMetadataXML(loaded_file_document);
        
    }

    // Determine the file's path relative to the location of the metadata.xml file
    String metadata_xml_file_directory_path = FilenameEncoding.fileToURLEncoding(getParentFile());
    String file_relative_path = file_node.getURLEncodedFilePath().substring(metadata_xml_file_directory_path.length());
    if (file_relative_path.startsWith(FilenameEncoding.URL_FILE_SEPARATOR)) {
        file_relative_path = file_relative_path.substring(FilenameEncoding.URL_FILE_SEPARATOR.length());
    }

    // Form a regular expression that specifies the scope of the metadata
    String file_path_regexp;
    if (file_relative_path.equals("")) {
        // Special case for matching all files in the directory
        file_path_regexp = DIRECTORY_FILENAME;
    }
    else {
        // Convert the file path into a regular expression that will match it
        file_path_regexp = MetadataTools.getRegularExpressionThatMatchesFilePath(file_relative_path);
    }

    //System.err.println("MetadataXMLFile.addMetadata() Adding meta for file regexp: "
    //  + file_path_regexp + " - " + org.greenstone.gatherer.util.Utility.debugUnicodeString(file_path_regexp));
    
    // Find the appropriate FileSet element for this file
    Element appropriate_fileset_element = null;

    // Read all the FileSet elements in the file
    NodeList fileset_elements_nodelist = loaded_file_document.getElementsByTagName(FILESET_ELEMENT);
    for (int i = 0; i < fileset_elements_nodelist.getLength(); i++) {
        Element current_fileset_element = (Element) fileset_elements_nodelist.item(i);

        // Check the FileName elements of the FileSet to see if we have a match
        NodeList filename_elements_nodelist = current_fileset_element.getElementsByTagName(FILENAME_ELEMENT);
        for (int j = 0; j < filename_elements_nodelist.getLength(); j++) {
        Element current_filename_element = (Element) filename_elements_nodelist.item(j);
        String current_filename_element_value = XMLTools.getElementTextValue(current_filename_element);

        // Only exact matches can be extended with new metadata
        if (current_filename_element_value.equals(file_path_regexp)) {
            appropriate_fileset_element = current_fileset_element;
            break;
        }
        }
    }

    // If no appropriate FileSet element exists create a new one for this file
    if (appropriate_fileset_element == null) {
        DebugStream.println("Creating new FileSet element for file since none exists..."+file_path_regexp);
        appropriate_fileset_element = loaded_file_document.createElement(FILESET_ELEMENT);

        Element new_filename_element = loaded_file_document.createElement(FILENAME_ELEMENT);
        new_filename_element.appendChild(loaded_file_document.createTextNode(file_path_regexp));
        appropriate_fileset_element.appendChild(new_filename_element);

        Element new_description_element = loaded_file_document.createElement(DESCRIPTION_ELEMENT);
        appropriate_fileset_element.appendChild(new_description_element);

        // add the fileset element for .* at the top: especially important for
        // non-accumulating (and override mode) meta. Other type fileset elements can be appended
        if(file_path_regexp.equals(DIRECTORY_FILENAME)) {
            loaded_file_document.getDocumentElement().insertBefore(appropriate_fileset_element,
                    loaded_file_document.getDocumentElement().getFirstChild());
        } else {
          loaded_file_document.getDocumentElement().appendChild(appropriate_fileset_element);
        }
    }

    // Add each of the metadata values to the FileSet's Description element
    Element description_element = (Element) appropriate_fileset_element.getElementsByTagName(DESCRIPTION_ELEMENT).item(0);
    for (int i = 0; i < metadata_values.size(); i++) {
        MetadataValue metadata_value = (MetadataValue) metadata_values.get(i);
        String metadata_element_name_full = metadata_value.getMetadataElement().getFullName();

        // Remove any characters that are invalid in XML
        String metadata_value_string = XMLTools.removeInvalidCharacters(metadata_value.getFullValue());

        // Square brackets need to be escaped because they are a special character in Greenstone
        metadata_value_string = metadata_value_string.replaceAll("\\[", "&#091;");
        metadata_value_string = metadata_value_string.replaceAll("\\]", "&#093;");

        // the gs.filenameEncoding metadata is unique in that, when added, removed or
        // changed, it must be applied on the file(name) whose metadata has been adjusted
        if(metadata_element_name_full.equals(FILENAME_ENCODING_METADATA)) {
            metadata_value_string = processFilenameEncoding(file_path_regexp, 
                                        file_node, metadata_value_string, false);
                              // true only if removing meta
        }

        // Check if this piece of metadata has already been assigned to this FileSet element
        boolean metadata_already_assigned = false;
        NodeList metadata_elements_nodelist = description_element.getElementsByTagName(METADATA_ELEMENT);
        for (int k = 0; k < metadata_elements_nodelist.getLength(); k++) {
        Element current_metadata_element = (Element) metadata_elements_nodelist.item(k);

        // Check if the metadata element name matches
        String current_metadata_element_name_full = current_metadata_element.getAttribute("name");
        if (current_metadata_element_name_full.equals(metadata_element_name_full)) {
          // if the metadata must not accumulate, then edit the current value
          if (!metadata_value.isAccumulatingMetadata()) {
            XMLTools.setNodeText(current_metadata_element, metadata_value_string);
            metadata_already_assigned = true;
            break;
          }
            // Check if the metadata element value matches
            String current_metadata_value_string = XMLTools.getElementTextValue(current_metadata_element);
            if (current_metadata_value_string.equals(metadata_value_string)) {
            // Metadata already assigned
            metadata_already_assigned = true;
            break;
            }
        }
        }

        // If the piece of metadata hasn't already been assigned, add it now
        if (!metadata_already_assigned) {
        // Create a new Metadata element to record this metadata
        Element new_metadata_element = loaded_file_document.createElement(METADATA_ELEMENT);
        new_metadata_element.setAttribute("name", metadata_value.getMetadataElement().getFullName());
        new_metadata_element.setAttribute("mode", (metadata_value.isAccumulatingMetadata() ? "accumulate" : "override"));
        new_metadata_element.appendChild(loaded_file_document.createTextNode(metadata_value_string));

        // Accumulating metadata: add at the end
        if (metadata_value.isAccumulatingMetadata()) {
            description_element.appendChild(new_metadata_element);
        }
        // Override metadata: add at the start (so it overrides inherited metadata without affecting other assigned metadata)
        else {
            description_element.insertBefore(new_metadata_element, description_element.getFirstChild());
        }
        }
    }

    // Remember that we've changed the file so it gets saved when a new one is loaded
    loaded_file_changed = true;
    }


    public ArrayList getMetadataAssignedToFile(File file, boolean fileEncodingOnly)
    {
    // If this metadata.xml file isn't the one currently loaded, load it now
    if (loaded_file != this) {
        // First we must save out the currently loaded file
        saveLoadedFile();

        // Parse the metadata.xml file
        Document document = XMLTools.parseXMLFile(this);
              if (document == null) {
        System.err.println("Error: Could not parse metadata.xml file " + getAbsolutePath());
        return new ArrayList();
        }

        loaded_file = this;
        loaded_file_document = document;
        
        reEncodeFilenamesInMetadataXML(loaded_file_document);
    }

    // Determine the file's path relative to the location of the metadata.xml file  
    String file_relative_path = FilenameEncoding.fileToURLEncoding(file);
    File metadata_xml_file_directory = getParentFile();
    String metadata_xml_file_directory_path = FilenameEncoding.fileToURLEncoding(metadata_xml_file_directory);
    file_relative_path = file_relative_path.substring(metadata_xml_file_directory_path.length());

    if (file_relative_path.startsWith(FilenameEncoding.URL_FILE_SEPARATOR)) {
        file_relative_path = file_relative_path.substring(FilenameEncoding.URL_FILE_SEPARATOR.length());
    }

    // Build up a list of metadata assigned to this file
    ArrayList metadata_values = new ArrayList();

    // Read all the FileSet elements in the file
    NodeList fileset_elements_nodelist = loaded_file_document.getElementsByTagName(FILESET_ELEMENT);
    for (int i = 0; i < fileset_elements_nodelist.getLength(); i++) {
        Element current_fileset_element = (Element) fileset_elements_nodelist.item(i);
        boolean current_fileset_matches = false;
        boolean is_one_file_only_metadata = true;
        File folder_metadata_inherited_from = null;

        // Check the FileName elements of the FileSet to see if we have a match
        NodeList filename_elements_nodelist = current_fileset_element.getElementsByTagName(FILENAME_ELEMENT);
        for (int j = 0; j < filename_elements_nodelist.getLength(); j++) {
        Element current_filename_element = (Element) filename_elements_nodelist.item(j);
        String current_filename_element_value = XMLTools.getElementTextValue(current_filename_element);

        //System.err.println("\n  Original TAIL filename was: " + Utility.debugUnicodeString(file.getName()));
        String hexdecoded_regexed_file_relative_path = FilenameEncoding.decodeStringContainingHexEntities(file_relative_path);
        //System.err.println("Looking in meta.xml for hexdecoded_regexed_file_RELATIVE_path: " + hexdecoded_regexed_file_relative_path
            //+ " - debug version: " + Utility.debugUnicodeString(hexdecoded_regexed_file_relative_path));      
    
        // Does this fileset specify metadata for one file only?
        is_one_file_only_metadata = true;
        if (current_filename_element_value.indexOf("*") != -1 && !current_filename_element_value.equals(DIRECTORY_FILENAME)) {
            // No, it specifies metadata for multiple files (but not all the files in the directory)
            is_one_file_only_metadata = false;
        }

        String hexdecoded_current_filename_element_value = FilenameEncoding.decodeStringContainingHexEntities(current_filename_element_value);
        //System.err.println("   Checking to see if it matches " + hexdecoded_current_filename_element_value + " - debug: " + Utility.debugUnicodeString(hexdecoded_current_filename_element_value));
            //System.err.println("   Checking to see if it matches " + current_filename_element_value + " - debug: " + Utility.debugUnicodeString(current_filename_element_value));
        
        // This fileset specifies metadata for the file
        // MetadataXMLFile.addMetadata(CollectionTreeNode, ArrayList) stored filename in uppercase hex
        // so need to make sure everything hex has been decoded (no more hex) to compare apples with apples     
        if (hexdecoded_regexed_file_relative_path.matches(hexdecoded_current_filename_element_value)) { //if (file_relative_path.matches(current_filename_element_value)) {
            //System.err.println("   @@@ Found a match in meta.xml for hexdecoded_regexed_file_relative_path: " + hexdecoded_regexed_file_relative_path);
            current_fileset_matches = true;
            if (!file_relative_path.equals("") && current_filename_element_value.equals(DIRECTORY_FILENAME)) {
            folder_metadata_inherited_from = metadata_xml_file_directory;
            }
            break;
        } //else {
            //System.err.println( hexdecoded_regexed_file_relative_path + " does not match " + hexdecoded_current_filename_element_value);
            //System.err.println( Utility.debugUnicodeString(hexdecoded_regexed_file_relative_path) + " does not match " + Utility.debugUnicodeString(hexdecoded_current_filename_element_value));
        //}
        
        // This fileset specifies metadata for the folder the file is in
        if (hexdecoded_regexed_file_relative_path.startsWith(hexdecoded_current_filename_element_value + FilenameEncoding.URL_FILE_SEPARATOR)) {
            current_fileset_matches = true;
            folder_metadata_inherited_from = new File(metadata_xml_file_directory, current_filename_element_value);
            break;
        }
        }

        // The FileSet doesn't apply, so move onto the next one
        if (current_fileset_matches == false) {
        continue;
        }

        // Read all the Metadata elements in the fileset
        NodeList metadata_elements_nodelist = current_fileset_element.getElementsByTagName(METADATA_ELEMENT);
        for (int k = 0; k < metadata_elements_nodelist.getLength(); k++) {
        Element current_metadata_element = (Element) metadata_elements_nodelist.item(k);
        String metadata_element_name_full = current_metadata_element.getAttribute("name");
        // if we're only looking for fileEncoding metadata and this isn't it, skip to the next
        if(fileEncodingOnly && !metadata_element_name_full.equals(FILENAME_ENCODING_METADATA)) {
            continue;
        }       
        String metadata_set_namespace = MetadataTools.getMetadataSetNamespace(metadata_element_name_full);

        // Ignore legacy crap
        if (metadata_set_namespace.equals("hidden")) {
            continue;
        }

        MetadataSet metadata_set = MetadataSetManager.getMetadataSet(metadata_set_namespace);
        if (metadata_set == null) {
            // The metadata set isn't loaded, so give the option of mapping the element into a loaded set
            String target_metadata_element_name_full = MetadataSetManager.mapUnloadedMetadataElement(metadata_element_name_full);
            if (target_metadata_element_name_full == null || target_metadata_element_name_full.equals("")) {
            // Skip this element if we still don't have a loaded element for it
            continue;
            }

            metadata_element_name_full = target_metadata_element_name_full;
            metadata_set_namespace = MetadataTools.getMetadataSetNamespace(metadata_element_name_full);
            metadata_set = MetadataSetManager.getMetadataSet(metadata_set_namespace);
        }

        MetadataElement metadata_element = MetadataTools.getMetadataElementWithName(metadata_element_name_full);

                String metadata_element_name = MetadataTools.getMetadataElementName(metadata_element_name_full);
        // If the element doesn't exist in the metadata set, we're not interested
                //Shaoqun modified. It needs to be added to metadata_set because the user might disable skim file   
        if (metadata_element == null) {
            metadata_element = metadata_set.addMetadataElementForThisSession(metadata_element_name);
            // continue;
        }

        // Square brackets need to be escaped because they are a special character in Greenstone
        String metadata_value_string = XMLTools.getElementTextValue(current_metadata_element);
        metadata_value_string = metadata_value_string.replaceAll("&#091;", "[");
        metadata_value_string = metadata_value_string.replaceAll("&#093;", "]");

        MetadataValueTreeNode metadata_value_tree_node = metadata_element.getMetadataValueTreeNode(metadata_value_string);

        // If there is no metadata value tree node for this value, create it
        if (metadata_value_tree_node == null) {
            DebugStream.println("Note: No value tree node for metadata value \"" + metadata_value_string + "\"");
            metadata_element.addMetadataValue(metadata_value_string);
            metadata_value_tree_node = metadata_element.getMetadataValueTreeNode(metadata_value_string);
        }

        MetadataValue metadata_value = new MetadataValue(metadata_element, metadata_value_tree_node);
        metadata_value.inheritsMetadataFromFolder(folder_metadata_inherited_from);
        metadata_value.setIsOneFileOnlyMetadata(is_one_file_only_metadata);

        // Is this accumulating metadata?
        if (current_metadata_element.getAttribute("mode").equals("accumulate")) {
            metadata_value.setIsAccumulatingMetadata(true);
        }

        // Add the new metadata value to the list
        metadata_values.add(metadata_value);
        }
    }

    return metadata_values;
    }


    public void removeMetadata(CollectionTreeNode file_node, ArrayList metadata_values)
    {
    // If this metadata.xml file isn't the one currently loaded, load it now
    if (loaded_file != this) {
        // First we must save out the currently loaded file
        saveLoadedFile();

        // Parse the metadata.xml file
        Document document = XMLTools.parseXMLFile(this);
        if (document == null) {
        System.err.println("Error: Could not parse metadata.xml file " + getAbsolutePath());
        return;
        }

        loaded_file = this;
        loaded_file_document = document;
        
        reEncodeFilenamesInMetadataXML(loaded_file_document);
    }

    // Determine the file's path relative to the location of the metadata.xml file
    String metadata_xml_file_directory_path = FilenameEncoding.fileToURLEncoding(getParentFile());
    String file_relative_path = file_node.getURLEncodedFilePath().substring(metadata_xml_file_directory_path.length());
    if (file_relative_path.startsWith(FilenameEncoding.URL_FILE_SEPARATOR)) {
        file_relative_path = file_relative_path.substring(FilenameEncoding.URL_FILE_SEPARATOR.length());
    }

    // Form a regular expression that specifies the scope of the metadata
    String file_path_regexp;
    if (file_relative_path.equals("")) {
        // Special case for matching all files in the directory
        file_path_regexp = DIRECTORY_FILENAME;
    }
    else {
        // Convert the file path into a regular expression that will match it
        file_path_regexp = MetadataTools.getRegularExpressionThatMatchesFilePath(file_relative_path);
    }

    // Find the appropriate FileSet element for this file
    Element appropriate_fileset_element = null;

    // Read all the FileSet elements in the file
    NodeList fileset_elements_nodelist = loaded_file_document.getElementsByTagName(FILESET_ELEMENT);
    for (int i = 0; i < fileset_elements_nodelist.getLength(); i++) {
        Element current_fileset_element = (Element) fileset_elements_nodelist.item(i);

        // Check the FileName elements of the FileSet to see if we have a match
        NodeList filename_elements_nodelist = current_fileset_element.getElementsByTagName(FILENAME_ELEMENT);
        for (int j = 0; j < filename_elements_nodelist.getLength(); j++) {
        Element current_filename_element = (Element) filename_elements_nodelist.item(j);
        String current_filename_element_value = XMLTools.getElementTextValue(current_filename_element);

        // Only exact matches can be extended with new metadata
        if (current_filename_element_value.equals(file_path_regexp)) {
            appropriate_fileset_element = current_fileset_element;
            break;
        }
        }
    }

    // If no appropriate FileSet element exists the metadata isn't assigned in this metadata.xml file
    if (appropriate_fileset_element == null) {
        DebugStream.println("Note: No appropriate FileSet element found when removing metadata from " + this);
        return;
    }

    // Remove each of the metadata values from the FileSet's Description element
    for (int i = 0; i < metadata_values.size(); i++) {
        MetadataValue metadata_value = (MetadataValue) metadata_values.get(i);

        // Remove any characters that are invalid in XML
        String metadata_value_string = XMLTools.removeInvalidCharacters(metadata_value.getFullValue());

        // Square brackets need to be escaped because they are a special character in Greenstone
        metadata_value_string = metadata_value_string.replaceAll("\\[", "&#091;");
        metadata_value_string = metadata_value_string.replaceAll("\\]", "&#093;");

        // Find the Metadata element to delete from the fileset
        String metadata_element_name_full = metadata_value.getMetadataElement().getFullName();
        NodeList metadata_elements_nodelist = appropriate_fileset_element.getElementsByTagName(METADATA_ELEMENT);
        for (int k = 0; k < metadata_elements_nodelist.getLength(); k++) {
        Element current_metadata_element = (Element) metadata_elements_nodelist.item(k);

        // Check the metadata element name matches
        String current_metadata_element_name_full = current_metadata_element.getAttribute("name");
        if (current_metadata_element_name_full.equals(metadata_element_name_full)) {
            // Check the metadata element value matches
            String current_metadata_value_string = XMLTools.getElementTextValue(current_metadata_element);
            if (current_metadata_value_string.equals(metadata_value_string)) {
            
            // Remove this Metadata element
            current_metadata_element.getParentNode().removeChild(current_metadata_element);
            
            // the gs.filenameEncoding metadata is unique in that, when added, removed or
            // changed, it must be applied on the file(name) whose metadata has been adjusted
            if(current_metadata_element_name_full.equals(FILENAME_ENCODING_METADATA)) {
            
                // metadata_value_string will hereafter be the inherited gs.FilenameEncoding 
                // metadata (if any), now that the value at this level has been removed
                metadata_value_string = processFilenameEncoding(file_path_regexp,
                        file_node, "", true); // true only if *removing* this meta  
            }
            
            // If there are no Metadata elements left now, remove the (empty) FileSet element
            if (metadata_elements_nodelist.getLength() == 0) {
                appropriate_fileset_element.getParentNode().removeChild(appropriate_fileset_element);
            }

            break;
            }
        }
        }
    }

    // Remember that we've changed the file so it gets saved when a new one is loaded
    loaded_file_changed = true;
    }


    public void replaceMetadata(CollectionTreeNode file_node, MetadataValue old_metadata_value, MetadataValue new_metadata_value)
    {
    // If this metadata.xml file isn't the one currently loaded, load it now
    if (loaded_file != this) {
        // First we must save out the currently loaded file
        saveLoadedFile();

        // Parse the metadata.xml file
        Document document = XMLTools.parseXMLFile(this);
        if (document == null) {
        System.err.println("Error: Could not parse metadata.xml file " + getAbsolutePath());
        return;
        }

        loaded_file = this;
        loaded_file_document = document;
        
        reEncodeFilenamesInMetadataXML(loaded_file_document);
    }

    // Determine the file's path relative to the location of the metadata.xml file
    String metadata_xml_file_directory_path = FilenameEncoding.fileToURLEncoding(getParentFile());
    String file_relative_path = file_node.getURLEncodedFilePath().substring(metadata_xml_file_directory_path.length());
    if (file_relative_path.startsWith(FilenameEncoding.URL_FILE_SEPARATOR)) {
        file_relative_path = file_relative_path.substring(FilenameEncoding.URL_FILE_SEPARATOR.length());
    }

    // Form a regular expression that specifies the scope of the metadata
    String file_path_regexp;
    if (file_relative_path.equals("")) {
        // Special case for matching all files in the directory
        file_path_regexp = DIRECTORY_FILENAME;
    }
    else {
        // Convert the file path into a regular expression that will match it
        file_path_regexp = MetadataTools.getRegularExpressionThatMatchesFilePath(file_relative_path);
    }

    // Remove any characters that are invalid in XML
    String old_metadata_value_string = XMLTools.removeInvalidCharacters(old_metadata_value.getFullValue());
    String new_metadata_value_string = XMLTools.removeInvalidCharacters(new_metadata_value.getFullValue());

    // Square brackets need to be escaped because they are a special character in Greenstone
    old_metadata_value_string = old_metadata_value_string.replaceAll("\\[", "&#091;");
    old_metadata_value_string = old_metadata_value_string.replaceAll("\\]", "&#093;");
    new_metadata_value_string = new_metadata_value_string.replaceAll("\\[", "&#091;");
    new_metadata_value_string = new_metadata_value_string.replaceAll("\\]", "&#093;");

    // Read all the FileSet elements in the file
    NodeList fileset_elements_nodelist = loaded_file_document.getElementsByTagName(FILESET_ELEMENT);
    for (int i = 0; i < fileset_elements_nodelist.getLength(); i++) {
        Element current_fileset_element = (Element) fileset_elements_nodelist.item(i);
        boolean current_fileset_matches = false;

        // Check the FileName elements of the FileSet to see if we have a match
        NodeList filename_elements_nodelist = current_fileset_element.getElementsByTagName(FILENAME_ELEMENT);
        for (int j = 0; j < filename_elements_nodelist.getLength(); j++) {
        Element current_filename_element = (Element) filename_elements_nodelist.item(j);
        String current_filename_element_value = XMLTools.getElementTextValue(current_filename_element);

        // Only exact matches can be edited
        if (current_filename_element_value.equals(file_path_regexp)) {
            current_fileset_matches = true;
            break;
        }
        }

        // The FileSet doesn't apply, so move onto the next one
        if (current_fileset_matches == false) {
        continue;
        }

        // Each metadata value is only allowed to be assigned once
        boolean new_metadata_value_already_exists = false;
        Element metadata_element_to_edit = null;

        // Find the Metadata element to replace in the fileset
        String metadata_element_name_full = old_metadata_value.getMetadataElement().getFullName();
        NodeList metadata_elements_nodelist = current_fileset_element.getElementsByTagName(METADATA_ELEMENT);
        for (int k = 0; k < metadata_elements_nodelist.getLength(); k++) {
        Element current_metadata_element = (Element) metadata_elements_nodelist.item(k);

        // Check the metadata element name matches
        String current_metadata_element_name_full = current_metadata_element.getAttribute("name");
        if (!current_metadata_element_name_full.equals(metadata_element_name_full)) {
            continue;
        }

        // Check the new metadata value doesn't already exist
        String current_metadata_value_string = XMLTools.getElementTextValue(current_metadata_element);
        if (current_metadata_value_string.equals(new_metadata_value_string)) {
            new_metadata_value_already_exists = true;
        }

        // Check the metadata element value matches
        if (current_metadata_value_string.equals(old_metadata_value_string)) {
            metadata_element_to_edit = current_metadata_element;
        }
        }

        // If the new metadata value already existed, remove the original value
        if (new_metadata_value_already_exists) {
            if(metadata_element_to_edit != null) { //?????????
                metadata_element_to_edit.getParentNode().removeChild(metadata_element_to_edit);
            } else {
                System.err.println("ERROR MetadataXMLFile: metadata_element_to_edit is null");
            }
        }
        // Otherwise replace the old value with the new value
        // Ensure metadata_element_to_edit isn't null (may occur when multiple files are selected)
        else if (metadata_element_to_edit != null) {
        
        // the gs.filenameEncoding metadata is unique in that, when added, removed or
        // changed, it must be applied on the file(name) whose metadata has been adjusted
        if(metadata_element_name_full.equals(FILENAME_ENCODING_METADATA)) {
            new_metadata_value_string = processFilenameEncoding(file_path_regexp, file_node, new_metadata_value_string, false);
            // true only if removing meta       
        }       
        XMLTools.setElementTextValue(metadata_element_to_edit, new_metadata_value_string);
        }
    }

    // Remember that we've changed the file so it gets saved when a new one is loaded
    loaded_file_changed = true;
    }


    static public void saveLoadedFile()
    {
    // If we have a file loaded into memory and it has been modified, save it now
    if (loaded_file != null && loaded_file_changed == true) {
        //System.err.println("START saveLoadedFile(), loaded_file_document:\n" + XMLTools.elementToString(loaded_file_document.getDocumentElement(), true));
        
        XMLTools.writeXMLFile(loaded_file, loaded_file_document, nonEscapingElements);
    
    /*  // DEBUGGING:
        Document doc = XMLTools.parseXMLFile(loaded_file);
        System.err.println("AT END saveLoadedFile(), PARSED loaded_file contains:\n" +  XMLTools.elementToString(doc.getDocumentElement(), true));
        
        reEncodeFilenamesInMetadataXML(doc);
        System.err.println("AT END saveLoadedFile(), RE-ENCODED loaded_file contains:\n" +  XMLTools.elementToString(doc.getDocumentElement(), true));
    */  
        loaded_file_changed = false;
    }
    
    //System.err.println("@@@@ END of saveLoadedFile()");
    //Utility.printCaller();
    }

    /** 
     * parseXML(metadata.xml) has the side-effect of resolving html entities.
     * Although this is not done by the GLIEntityResolver usage in parseXML(), something
     * in parseXML() is resolving the html entities, including those used in carefully
     * html-entity-escaped filenames.
     * We need to get the filenames in the DOM correct after parsing a metadata.xml file
     * into memory, so that we have the correct filenames and so that we'll write it out correctly.
     * Therefore, always call this method after a successful parseXML() call on a metadata.xml.
     * @param doc is the Document where the FILENAME_ELEMENTs need to be re-encoded.
     * At the end of this function, the doc will be modified with the re-encoded filenames.
     * 
    */
    static private void reEncodeFilenamesInMetadataXML(Document doc) {
        if(!FilenameEncoding.MULTIPLE_FILENAME_ENCODINGS_SUPPORTED) {
            return;
        }
        
        //System.err.println("PARSED loaded_file contains:\n" +  XMLTools.elementToString(doc.getDocumentElement(), true));
        
        // Read all the FileSet elements in the file
        NodeList fileset_elements_nodelist = doc.getElementsByTagName(FILESET_ELEMENT);
        for (int i = 0; i < fileset_elements_nodelist.getLength(); i++) {
            Element current_fileset_element = (Element) fileset_elements_nodelist.item(i);

            // get the value of all FileName elements
            NodeList filename_elements_nodelist = current_fileset_element.getElementsByTagName(FILENAME_ELEMENT);
            for (int j = 0; j < filename_elements_nodelist.getLength(); j++) {
                Element filename_element = (Element) filename_elements_nodelist.item(j);
                String filename = XMLTools.getElementTextValue(filename_element);
                if(!filename.equals(DIRECTORY_FILENAME)) {
                    //System.err.println("Filename before reencoding was: " + filename);
                    // reencode filename                    
                    // can't convert to URI with backslash-escaped chars (backslash used in regexed filename are illegal in URI object
                    // created by filenameToURLEncoding).
                    String encoded_filename = filename.replace("\\", "%5C"); 
                    encoded_filename = FilenameEncoding.filenameToURLEncoding(encoded_filename);
                    // escape chars for regex again
                    encoded_filename = encoded_filename.replace("%5C", "\\");
                    XMLTools.setElementTextValue(filename_element, encoded_filename);
                    //System.err.println("Filename after reencoding was: " + encoded_filename);
                }
            }
        }       
        //System.err.println("RE-ENCODED loaded_file contains:\n" +  XMLTools.elementToString(doc.getDocumentElement(), true));
    }
    
    /**
     * Every metadata.xml file must be skimmed when a collection is opened, for three very important reasons:
     *   - To handle any non-namespaced metadata in the metadata.xml files (this is mapped and the files rewritten)
     *   - To get a complete list of the metadata elements in the collection (used in Design and Format panes)
     *   - To build complete and accurate metadata value trees (used in the Enrich pane)
     */
    public void skimFile()
    {
    boolean file_changed = false;

    // Parse the metadata.xml file
    DebugStream.println("Skimming metadata.xml file " + this + "...");
           
    Document document = XMLTools.parseXMLFile(this);
    if (document == null) {
        System.err.println("Error: Could not parse metadata.xml file " + getAbsolutePath());
        return;
    }
    // Always call this method after calling parseXMLFile
    reEncodeFilenamesInMetadataXML(document);
    
    // Read all the Metadata elements in the file
    HashMap target_metadata_element_name_attrs_cache = new HashMap();
    NodeList metadata_elements_nodelist = document.getElementsByTagName(METADATA_ELEMENT);
    for (int i = 0; i < metadata_elements_nodelist.getLength(); i++) {
        Element current_metadata_element = (Element) metadata_elements_nodelist.item(i);
        String metadata_element_name_full = current_metadata_element.getAttribute("name");
        String metadata_set_namespace = MetadataTools.getMetadataSetNamespace(metadata_element_name_full);

        // Ignore legacy crap
        if (metadata_set_namespace.equals("hidden")) {
        continue;
        }

        MetadataSet metadata_set = MetadataSetManager.getMetadataSet(metadata_set_namespace);
        if (metadata_set == null) {
        // The metadata set isn't loaded, so give the option of mapping the element into a loaded set
        String target_metadata_element_name_full = MetadataSetManager.mapUnloadedMetadataElement(metadata_element_name_full);
        if (target_metadata_element_name_full == null || target_metadata_element_name_full.equals("")) {
            // Skip this element if we still don't have a loaded element for it
            continue;
        }

        // Update the metadata.xml file to have the new (namespaced) element name
        // Instead of using current_metadata_element.setAttribute("name", target_metadata_element_name_full)
        //   we create an Attr object for each target metadata element name, and cache them
        // This makes a *huge* difference (namespacing a metadata.xml file with 45000 metadata entries now
        //   takes 45 seconds instead of 30 minutes!) -- why is setting the value of a Node so slow?
        Attr target_metadata_element_name_attr = (Attr) target_metadata_element_name_attrs_cache.get(target_metadata_element_name_full);
        if (target_metadata_element_name_attr == null) {
            target_metadata_element_name_attr = document.createAttribute("name");
            target_metadata_element_name_attr.setValue(target_metadata_element_name_full);
            target_metadata_element_name_attrs_cache.put(target_metadata_element_name_full, target_metadata_element_name_attr);
        }

        // Remove the old name attribute and add the new (namespaced) one
        current_metadata_element.removeAttribute("name");
        current_metadata_element.setAttributeNode((Attr) target_metadata_element_name_attr.cloneNode(false));
        file_changed = true;

        metadata_element_name_full = target_metadata_element_name_full;
        metadata_set_namespace = MetadataTools.getMetadataSetNamespace(metadata_element_name_full);
        metadata_set = MetadataSetManager.getMetadataSet(metadata_set_namespace);
        }

        String metadata_element_name = MetadataTools.getMetadataElementName(metadata_element_name_full);
        MetadataElement metadata_element = metadata_set.getMetadataElementWithName(metadata_element_name);

        // If the element doesn't exist in the metadata set, add it
        if (metadata_element == null) {
        metadata_element = metadata_set.addMetadataElementForThisSession(metadata_element_name);
        }

        // Square brackets need to be escaped because they are a special character in Greenstone
        String metadata_value_string = XMLTools.getElementTextValue(current_metadata_element);
        metadata_value_string = metadata_value_string.replaceAll("&#091;", "[");
        metadata_value_string = metadata_value_string.replaceAll("&#093;", "]");

        metadata_element.addMetadataValue(metadata_value_string);
    }

    // Rewrite the metadata.xml file if it has changed
    if (file_changed) {
        XMLTools.writeXMLFile(this, document);
    }
    }

    /** 
     * The gs.filenameEncoding metadata is unique in that, when added, removed or
     * replaced, it must be applied on the file(name) whose metadata has been 
     * adjusted. 
     * This method handles all that, given the regular expression or filepath name 
     * to match on (.* matches subdirectories), the affected fileNode, the new 
     * encoding value and whether a new encoding value has been added/an existing
     * one has been replaced or whether the encoding metadata has been removed.
     * The new adjusted value for the encoding metadata is returned.
     *
     * MetadataXMLFileManager maintains a hashmap of (URL-encoded filepaths, encoding) 
     * to allow fast access to previously assigned gs.filenameEncoding metadata (if
     * any) for each file. This hashmap also needs to be updated, but this update
     * is complicated by the fact that it concerns regular expressions that could
     * affect multiple filenames.
     */
    public String processFilenameEncoding(String file_path_regexp, CollectionTreeNode file_node, 
                    String encoding_metadata_value, boolean removingMetadata) 
    {
        if(!FilenameEncoding.MULTIPLE_FILENAME_ENCODINGS_SUPPORTED) {
            return encoding_metadata_value;
        }

        // Work out this filenode's new encoding and apply it:
        
        if(removingMetadata) { // encoding_metadata_value = ""
            // gs.filenameEncoding metadata being removed, work out 
            // any inherited metadata to replace it with in the meta-table
            encoding_metadata_value = FilenameEncoding.getInheritedFilenameEncoding(
                        file_node.getURLEncodedFilePath(), file_node.getFile());
            // should be canonical encoding already
        } 
        else if(!encoding_metadata_value.equals("")) { 
            // if adding or replacing filename encoding,
            // get the canonical encoding name for this alias
            encoding_metadata_value = FilenameEncoding.canonicalEncodingName(encoding_metadata_value);
        }   
        // Reencode the display of this filenode only as any affected 
        // childnodes will be reencoded on FileNode.refreshDescendantEncodings()
        file_node.reencodeDisplayName(encoding_metadata_value);
            

        // Whether removing or adding/replacing the file's gs.filename encoding meta,
        // store this in the file-to-encoding map for fast access, since the map stores
        // empty string values when no meta has been assigned at this file level.
        // In the case of removingMetadata, the value stored will be the fallback value
        
        String urlpath = file_node.getURLEncodedFilePath();
        if(removingMetadata) { 
            // remove it from the map instead of inserting "", so that when folders in the collectiontree 
            // are being deleted or shifted, the removemetada (and addmetadata) calls that get fired 
            // for each affected filenodes does not cause the undesirable effect of multiple "" to be 
            // entered into the filename-to-encoding map for filepaths that no longer exist .
            FilenameEncoding.map.remove(urlpath); 
        } else { // for adding and replacing, put the encoding into the map (also replaces any existing encoding for it)
            FilenameEncoding.map.put(urlpath, encoding_metadata_value);         
        }
        
        // If new folder-level metadata (or metadata for a set of files fitting a pattern) has been
        //  assigned, the file_to_encodings map will be cleared for all descendant folders and files,
        //  so that these can be re-calculated upon refreshing the visible parts of the CollectionTree. 
        // Mark the state as requiring a refresh of the CollectionTree. 
        // This next step also serves to prevent the MetadataValueTableModel from trying to update
        // itself while a refresh (involving re-encoding of filenames of visible nodes) is in progress.
        FilenameEncoding.setRefreshRequired(true);
        
        return encoding_metadata_value;
    }
}