source: trunk/gli/src/org/greenstone/gatherer/collection/CollectionManager.java@ 7161

/**
 *#########################################################################
 *
 * A component of the Gatherer application, part of the Greenstone digital
 * library suite from the New Zealand Digital Library Project at the
 * University of Waikato, New Zealand.
 *
 * <BR><BR>
 *
 * Author: John Thompson, Greenstone Digital Library, University of Waikato
 *
 * <BR><BR>
 *
 * Copyright (C) 1999 New Zealand Digital Library Project
 *
 * <BR><BR>
 *
 * 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.
 *
 * <BR><BR>
 *
 * 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.
 *
 * <BR><BR>
 *
 * 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.collection;

import java.io.*;
import java.lang.Class;
import java.util.*;
import javax.swing.*;
import javax.swing.event.*;
import javax.swing.filechooser.FileSystemView;
import javax.swing.tree.*;
import org.greenstone.gatherer.Dictionary;
import org.greenstone.gatherer.Gatherer;
import org.greenstone.gatherer.cdm.CollectionDesignManager;
import org.greenstone.gatherer.cdm.CollectionMeta;
import org.greenstone.gatherer.cdm.CollectionMetaManager;
import org.greenstone.gatherer.collection.BasicCollectionConfiguration;
import org.greenstone.gatherer.collection.Collection;
import org.greenstone.gatherer.collection.SaveCollectionTask;
import org.greenstone.gatherer.file.FileNode;
import org.greenstone.gatherer.file.FileSystemModel;
import org.greenstone.gatherer.gui.LockFileDialog;
import org.greenstone.gatherer.gui.NewCollectionMetadataPrompt;
import org.greenstone.gatherer.gui.ExternalCollectionPrompt;
import org.greenstone.gatherer.gui.NewMetaSetPrompt;
import org.greenstone.gatherer.gui.WarningDialog;
import org.greenstone.gatherer.gui.tree.WorkspaceTree;
import org.greenstone.gatherer.msm.ElementWrapper;
import org.greenstone.gatherer.msm.MetadataXMLFileManager;
import org.greenstone.gatherer.msm.GreenstoneArchiveParser;
import org.greenstone.gatherer.msm.LegacyCollectionImporter;
import org.greenstone.gatherer.msm.MetadataSet;
import org.greenstone.gatherer.msm.MetadataSetManager;
import org.greenstone.gatherer.msm.MSMEvent;
import org.greenstone.gatherer.msm.MSMListener;
import org.greenstone.gatherer.msm.MSMProfiler;
import org.greenstone.gatherer.msm.MSMUtils;
import org.greenstone.gatherer.shell.GShell;
import org.greenstone.gatherer.shell.GShellEvent;
import org.greenstone.gatherer.shell.GShellListener;
import org.greenstone.gatherer.shell.GShellProgressMonitor;
import org.greenstone.gatherer.undo.UndoManager;
import org.greenstone.gatherer.util.ArrayTools;
import org.greenstone.gatherer.util.Codec;
import org.greenstone.gatherer.util.GSDLSiteConfig;
import org.greenstone.gatherer.util.StaticStrings;
import org.greenstone.gatherer.util.SynchronizedTreeModelTools;
import org.greenstone.gatherer.util.Utility;
import org.w3c.dom.*;

/** This class manages many aspects of the collection, from its creation via scripts, data access via methods and its importing and building into the final collection. It is also resposible for firing appropriate event when significant changes have occured within the collection, and for creating a new metadata set manager as necessary.
 * @author John Thompson
 * @version 2.3
 */
public class CollectionManager
    implements GShellListener, MSMListener {
    /** A reference to the metadata set manager. */
    public MetadataSetManager msm;
    /** A reference to the undo manager. Although only one instance is shared between all collections, the undo queues are emptied between each. */
    public UndoManager undo;
    /** Are we currently in the process of building? */
    private boolean building = false;
    /** Are we currently in the process of importing? */
    private boolean importing = false;
    /** The collection this manager is managing! */
    static private Collection collection = null;
    /** The collection_model. */
    private FileSystemModel collection_model = null;
    /** The workspace model. This becomes invalid on a collection change. */
    // private FileSystemModel workspace_model = null;
    /** An inner class listener responsible for noting tree changes and resetting saved when they occur. */
    private FMTreeModelListener fm_tree_model_listener = null;
    /** The monitor resposible for parsing the build process. */
    private GShellProgressMonitor build_monitor = null;
    /** The monitor resposible for parsing the import process. */
    private GShellProgressMonitor import_monitor = null;

    /** Holds a reference to the thread responsible for closing the collection. If non-null then only calls from the given thread will see the collection is non-ready. All other threads will have to wait until closing thread, and all of it consequential calls, are completely finished. */
    private Thread closing_thread = null;

    /** The name of the standard lock file. */
    static final public String LOCK_FILE = "gli.lck";

    /** Used to indicate the source of the message is the file collection methods. */
    static final public int COLLECT   = 3;
    /** Used to indicate the source of the message is the building methods. */
    static final public int BUILDING  = 5;

    /** Constructor. */
    public CollectionManager() {
    // Initialisation.
    this.building = false;
    this.importing = false;
    this.collection = null;
    this.undo = new UndoManager();
    }
    /** Add a special directory mapping.
     * @param name The name for this directory mapping as a <strong>String</strong>.
     * @param file The directory this mapping maps to as a <strong>File</strong>.
     */
    public void addDirectoryMapping(String name, File file) {
    // Update the information stored in the Gatherer config
    Gatherer.config.addDirectoryMapping(name, file);
    // Now update the tree
    Gatherer.g_man.gather_pane.refreshWorkspaceTree(WorkspaceTree.MAPPED_DIRECTORIES_CHANGED);
    }
    /** This method calls the builcol.pl scripts via a GShell so as to not lock up the processor.
     * @see org.greenstone.gatherer.Configuration
     * @see org.greenstone.gatherer.Gatherer
     * @see org.greenstone.gatherer.collection.Collection
     * @see org.greenstone.gatherer.gui.BuildOptions
     * @see org.greenstone.gatherer.shell.GShell
     * @see org.greenstone.gatherer.shell.GShellListener
     * @see org.greenstone.gatherer.shell.GShellProgressMonitor
     * @see org.greenstone.gatherer.util.Utility
     */
    public void buildCollection() {
    Gatherer.println("CollectionManager.buildCollection()");
    building = true;
    String lang = Gatherer.config.getLanguage();
    String args[];
    if(Utility.isWindows()) {
        args = new String[7];
        args[0] = Gatherer.config.perl_path;
        args[1] = "-S";
        args[2] = Gatherer.config.getScriptPath() + "buildcol.pl";
        args[3] = "-gli";
        args[4] = "-language";
        args[5] = lang;
        args[6] = collection.getName();
    }
    else {
        args = new String[5];
        args[0] = Gatherer.config.getScriptPath() + "buildcol.pl";
        args[1] = "-gli";
        args[2] = "-language";
        args[3] = lang;
        args[4] = collection.getName();
    }
    args = ArrayTools.add(args, collection.build_options.getBuildValues());
    GShell shell = new GShell(args, GShell.BUILD, BUILDING, this, build_monitor, GShell.GSHELL_BUILD);
    shell.addGShellListener(Gatherer.g_man.create_pane);
    shell.start();
    Gatherer.println("CollectionManager.buildCollection().return");
    }

    /** Used to determine whether the currently active collection has been built.
     * @return A boolean indicating the built status of the collection.
     */
    public boolean built() {
    if(collection != null) {
        // Determine if the collection has been built by looking for the build.cfg file
        File build_cfg_file = new File(getCollectionIndex() + Utility.BUILD_CFG_FILENAME);
        return build_cfg_file.exists();
    }
    return false;
    }

    /** a test method to see if we can delete a directory/file - returns false is the file or any of the contents of a directory cannot be deleted */
    public boolean canDelete(File file) {
    if (!file.isDirectory()) {
        return file.canWrite();
    }
    File [] file_list = file.listFiles();
    for (int i=0; i<file_list.length; i++) {
        if (!canDelete(file_list[i])) {
        return false;
        }
    }
    return true;
    }
    /** Called to close the current collection and remove its lock file.
     * @see org.greenstone.gatherer.Gatherer
     * @see org.greenstone.gatherer.collection.Collection
     * @see org.greenstone.gatherer.util.Utility
     */
    public void closeCollection() {
    Gatherer.println("Close collection: " + collection.getName());
    // We set the closing thread, as it should be the only one who can actually see the collection is closed, at least until the closing thread expires.
    closing_thread = Thread.currentThread();
    // Remove the lock on this file, then remove the collection.
    File lock_file = new File(Utility.getCollectionDir(Gatherer.config.gsdl_path) + collection.getName() + File.separator + LOCK_FILE);
    lock_file.delete();
    if(lock_file.exists()) {
       System.err.println("Lockfile was not successfully deleted.");
    }
    collection.msm.destroy();
    collection = null;
    collection_model = null;
    // workspace_model = null;
    undo.clear();
    Gatherer.config.setCollectionConfiguration(null);
    Gatherer.g_man.collectionChanged(false);
    // All of the consequences of a close should have been processed by now, so others should now see the collection as non-ready.
    closing_thread = null;
    }

    /** Method that is called whenever something has changed in the configuration of this collection. */
    public void configurationChanged() {
    if(collection != null) {
        collection.setSaved(false);
    }
    }

    /** Used to set the current collection to the given collection. Note that this call should -always- be proceeded by a ready call, and if the colection is ready and the saved flag is unset then the user should be prompted to save. Also note that this method creates yet another GShell to run buildcol.pl.
     * @param description a description of the collection as a String
     * @param email the email address of the author/maintainer as a String
     * @param name the short name of the collection, which will subsequently be used to refer to this particular collection, as a String
     * @param title the longer title of the collection as a String
     * @param base_collection_directory if the user has chosen to base their new collection on an existing one, this is the directory where this base collection can be found, as a File, otherwise its null
     * @param metadata_sets if the user has decided to select several metadata sets with which to initially populate the GLI then this is an ArrayList of metadata set file names, otherwise its null
     */
    public void createCollection(String description, String email, String name, String title, File base_collection_directory, ArrayList metadata_sets) {
    boolean cancelled = false;

    try {
        // Create a progress monitor.
        ProgressMonitor progress = new ProgressMonitor(Gatherer.g_man, Dictionary.get("CollectionManager.Creating_New"), "mkcol.pl", 0, 7);
        // Create the new collection.
        makeCollection(description, email, name, title);
        progress.setProgress(1);

        String a_dir = Utility.getCollectionDir(Gatherer.config.gsdl_path) + name + File.separator;

        // ACTIVE_DIR/log/
        File log_dir_temp = new File(Utility.getLogDir(a_dir)+"temp.dat");
        File log_dir = log_dir_temp.getParentFile();
        log_dir.mkdirs();
        if(progress != null) {
        progress.setNote(Dictionary.get("CollectionManager.Log_Created"));
        }

        progress.setProgress(2);

        // Now create the collection object around the directory.
        collection = new Collection(new File(a_dir, name + ".col"));
        collection.msm = new MetadataSetManager();
        msm = collection.msm; // Legacy
        collection.msm.load();

        // Import default metadata sets if any.
        for(int i = 0; metadata_sets != null && i < metadata_sets.size(); i++) {
        MetadataSet metadata_set = (MetadataSet) metadata_sets.get(i);
        collection.msm.importMDS(metadata_set.getFile(), false);
        }

        boolean skip_import_phase = false;

        // Before we create the CollectionDesignManager we have to check if we are basing it upon some other collection.
        if(base_collection_directory != null) {
           Gatherer.println("Basing new collection on existing one: " + base_collection_directory);
           collection.setBaseCollection(base_collection_directory.getAbsolutePath());
        // Try to import any existing metadata sets for this collection. Look in base_collection_directory/metadata and import any metadata sets found.
        File base_metadata = new File(base_collection_directory, Utility.META_DIR);
        if(base_metadata.exists()) {
            Gatherer.println("Found the metadata directory.");
            File[] possible_metadata_sets = base_metadata.listFiles();
            for(int i = 0; possible_metadata_sets != null && i < possible_metadata_sets.length; i++) {
            String filename = possible_metadata_sets[i].getName();
            if(filename.endsWith(".mds")) {
                Gatherer.println("+ Found a metadata set. Importing: " + possible_metadata_sets[i].getAbsolutePath());
                collection.msm.importMDS(possible_metadata_sets[i], false);
                skip_import_phase = true;
            }
            }
        }
        else {
            Gatherer.println("This base collection has no metadata directory.");
        }
        // If no sets were imported, then create a new metadata with this new collections name.
        if(collection.msm.getSets().size() == 0) {
            // Prompt the user so that they can choose at least one initial metadata set. We're sneaky here and just create a ncm_prompt
            Gatherer.println("This collection has no metadata sets. Present the user with the metadata set selection prompt.");
            NewCollectionMetadataPrompt ncm_prompt = new NewCollectionMetadataPrompt();
            // If cancelled then they really do mean to start a collection with no metadata sets.
            if(!ncm_prompt.isCancelled()) {
            ArrayList initial_sets = ncm_prompt.getSets();
            for(int i = 0; initial_sets != null && i < initial_sets.size(); i++) {
                MetadataSet metadata_set = (MetadataSet) initial_sets.get(i);
                collection.msm.importMDS(metadata_set.getFile(), false);
                metadata_set = null;
            }
            initial_sets = null;
            }
            ncm_prompt.dispose();
            ncm_prompt = null;
        }
        // Do a dry metadata import run over the entire base collection, recording profile mappings. We do this by finding the archive files, and then iterating over them using the GreenstoneArchiveParser to retrieve metadata from them. We then process the importing of new metadata elements using the selectElement prompt used in a file action metadata import. However the big change is that we don't actually import any metadata, just create importing profiles.
        if(!skip_import_phase) {
            File base_archive = new File(base_collection_directory, Utility.ARCHIVE_DIR);
            if(base_archive.exists()) {
            Gatherer.println("+ Archive directory found. Inspecting archives for metadata information.");
            ArrayList metadata_elements = GreenstoneArchiveParser.extractMetadataElements(base_archive);
            for(int i = 0; !cancelled && i < metadata_elements.size(); i++) {
                String metadata_name = (String) metadata_elements.get(i);
                ElementWrapper target = collection.msm.prompt.selectElement(metadata_name);
                cancelled = Gatherer.c_man.getCollection().msm.prompt.wasDialogCancelled();
                if(!cancelled) {
                if(target != null) {
                    collection.msm.profiler.addAction(base_collection_directory.getAbsolutePath(), metadata_name, target.getName());
                }
                else {
                    collection.msm.profiler.addAction(base_collection_directory.getAbsolutePath(), metadata_name, null);
                }
                }
            }
            // Hopefully mappings should now be in place for metadata extracted from this collection.
            }
            else {
            Gatherer.println("+ Searching files for metadata.xml information.");
            // Find the import directory
            File base_import = new File(base_collection_directory, Utility.IMPORT_DIR);
            if(base_import.exists()) {
                searchForMetadata(base_import);
            }
            }
        }
        // And if that fails then we must have been asked by Satan himself to build the very digital collections of hell, because they don't match any goodly greenstone collection I have ever seen, so you can't blame me if I can't import them.

        // Now we update our collect.cfg
        Gatherer.println("Copy and update collect.cfg from base collection.");
        updateCollectionCFG(new File(base_collection_directory, Utility.CONFIG_DIR), new File(a_dir, Utility.CONFIG_DIR), description, email, title);
        }

        // Always import the extracted metadata set if we didn't already
        if(collection.msm.getSet(Utility.EXTRACTED_METADATA_NAMESPACE) == null) {
           collection.msm.importMDS(new File(Utility.METADATA_DIR + Utility.EXTRACTED_METADATA_NAMESPACE + StaticStrings.METADATA_SET_EXTENSION), false);
        }

        collection.cdm = new CollectionDesignManager(new File(getCollectionConfig()));

        // Now that we have a CDM, update several settings, such as if we created this collection by basing it on another, set it as public automatically
        if(base_collection_directory != null) {
            // Update the creator and maintainer
            CollectionMeta creator_collectionmeta = new CollectionMeta(collection.cdm.collect_config.getCreator());
            creator_collectionmeta.setValue(email);
            creator_collectionmeta = null;
            CollectionMeta maintainer_collectionmeta = new CollectionMeta(collection.cdm.collect_config.getMaintainer());
            maintainer_collectionmeta.setValue(email);
            maintainer_collectionmeta = null;
            // Update the collection title
            CollectionMeta collection_name_collectionmeta = collection.cdm.collectionmeta_manager.getMetadatum(StaticStrings.COLLECTIONMETADATA_COLLECTIONNAME_STR);
            collection_name_collectionmeta.setValue(title);
            collection_name_collectionmeta = null;
            // And now the description
            CollectionMeta collection_extra_collectionmeta = collection.cdm.collectionmeta_manager.getMetadatum(StaticStrings.COLLECTIONMETADATA_COLLECTIONEXTRA_STR);
            collection_extra_collectionmeta.setValue(description);
            collection_extra_collectionmeta = null;
            // All collections based on others are automatically public
            CollectionMeta public_collectionmeta = new CollectionMeta(collection.cdm.collect_config.getPublic());
            public_collectionmeta.setValue(StaticStrings.TRUE_STR);
            public_collectionmeta = null;
            // Finally reset the icons
            CollectionMeta icon_collection_collectionmeta = collection.cdm.collectionmeta_manager.getMetadatum(StaticStrings.COLLECTIONMETADATA_ICONCOLLECTION_STR);
            icon_collection_collectionmeta.setValue(StaticStrings.EMPTY_STR);
            icon_collection_collectionmeta = null;
            CollectionMeta icon_collection_small_collectionmeta = collection.cdm.collectionmeta_manager.getMetadatum(StaticStrings.COLLECTIONMETADATA_ICONCOLLECTIONSMALL_STR);
            icon_collection_small_collectionmeta.setValue(StaticStrings.EMPTY_STR);
            icon_collection_small_collectionmeta = null;
        }

        collection.gdm = new MetadataXMLFileManager();

        progress.setProgress(3);

        // Has to be done after creating metadata set manager.
        File gmeta_dir_temp = new File(getCollectionMetadata()+"temp.dat");
        File gmeta_dir = gmeta_dir_temp.getParentFile();
        gmeta_dir.mkdirs();
        if(progress != null) {
        progress.setNote("GMeta created");
        }
        progress.setProgress(4);

        progress.setProgress(6);
        // Register ourselves as being interested in what the msm has to say.
        collection.msm.addMSMListener(this);
        // Create a lock file.
        File lock_file = new File(a_dir, LOCK_FILE);
        FileOutputStream out = new FileOutputStream(lock_file);
        out.write(LOCK_FILE.getBytes());
        out.close();
        out = null;
        progress.setProgress(7);
        String args[] = new String[1];
        args[0] = name;
        progress.setNote(Dictionary.get("CollectionManager.Session_Ready", args));
        progress.close();
    }
    catch (Exception error) {
        Gatherer.printStackTrace(error);
    }
    // Done.
    if(Gatherer.g_man != null) {
        // workspace_model = null;
        // set the view to Gather pane
        Gatherer.g_man.setSelectedView(Gatherer.g_man.gather_pane);
        Gatherer.g_man.collectionChanged(ready());
    }
    }

    public void createLockFile(File destination) {
    try {
        Document default_lockfile = Utility.parse("xml/" + LOCK_FILE, true);
        String user_name = System.getProperty("user.name");
        Element person_element = (Element) MSMUtils.getNodeFromNamed(default_lockfile.getDocumentElement(), "User");
        person_element.appendChild(default_lockfile.createTextNode(user_name));
        person_element = null;
        user_name = null;
        String machine_name = Utility.getMachineName();
        Element machine_element = (Element) MSMUtils.getNodeFromNamed(default_lockfile.getDocumentElement(), "Machine");
        machine_element.appendChild(default_lockfile.createTextNode(machine_name));
        machine_element = null;
        machine_name = null;
        String date_time = Utility.getDateString();
        Element date_element = (Element) MSMUtils.getNodeFromNamed(default_lockfile.getDocumentElement(), "Date");
        date_element.appendChild(default_lockfile.createTextNode(date_time));
        date_element = null;
        date_time = null;
        Utility.export(default_lockfile, destination);
    }
    catch (Exception error) {
        Gatherer.printStackTrace(error);
    }
    }

    /** Method that is called whenever an element within a set is changed or modified. We want to mark the collection so that it needs saving again.
     * @param event A <strong>MSMEvent</strong> containing details of the event that caused this message to be fired.
     * @see org.greenstone.gatherer.collection.Collection
     */
    public void elementChanged(MSMEvent event) {
    // This means the state of the collections has changed, so we should set saved to false.
    collection.setSaved(false);
    }
    /** Used to retrieve the build options associated with the currently loaded collection. If none yet exist, default ones are created.
     * @return A <strong>BuildOptions</strong> object containing the build options for the current collection.
     * @see org.greenstone.gatherer.collection.Collection
     */
    /* private BuildOptions getBuildOptions() {
    return collection.build_options;
    } */

    /** Retrieve the current collection.
     * @return The <strong>Collection</strong> itself.
     */
    public Collection getCollection() {
    return collection;
    }
    /** Constructs the absolute filename of the collection archive directory, which should resemble "$GSDLHOME/collect/&lt;col_name&gt;/archive/"
     * @return A <strong>String</strong> containing the filename.
     * @see org.greenstone.gatherer.Configuration
     * @see org.greenstone.gatherer.Gatherer
     * @see org.greenstone.gatherer.collection.Collection
     * @see org.greenstone.gatherer.util.Utility
     */
    public String getCollectionArchive() {
    return Utility.getArchiveDir(Gatherer.config.gsdl_path, collection.getName());
    }
    /** Constructs the absolute filename of the collection building directory, which should resemble "$GSDLHOME/collect/&lt;col_name&gt;/building/"
     * @return A <strong>String</strong> containing the filename.
     * @see org.greenstone.gatherer.Configuration
     * @see org.greenstone.gatherer.Gatherer
     * @see org.greenstone.gatherer.collection.Collection
     * @see org.greenstone.gatherer.util.Utility
     */
    public String getCollectionBuild() {
    return Utility.getBuildDir(Utility.getCollectionDir(Gatherer.config.gsdl_path) + collection.getName() + File.separator);
    }

    /** Constructs the absolute filename of the collection config file, which should resemble "$GSDLHOME/collect/&lt;col_name&gt;/etc/collect.cfg"
     * @return A <strong>String</strong> containing the filename.
     * @see org.greenstone.gatherer.Configuration
     * @see org.greenstone.gatherer.Gatherer
     * @see org.greenstone.gatherer.collection.Collection
     * @see org.greenstone.gatherer.util.Utility
     */
    public String getCollectionConfig() {
    return Utility.getConfigDir(Utility.getCollectionDir(Gatherer.config.gsdl_path) + collection.getName() + File.separator);
    }

    /** Constructs the absolute filename of the collection directory, which should resemble "$GSDLHOME/collect/&lt;col_name&gt;"
     * @return A <strong>String</strong> containing the directory name.
     * @see org.greenstone.gatherer.Configuration
     * @see org.greenstone.gatherer.Gatherer
     * @see org.greenstone.gatherer.collection.Collection
     * @see org.greenstone.gatherer.util.Utility
     */
    public String getCollectionDirectory() {
    return Utility.getCollectionDir(Gatherer.config.gsdl_path) + collection.getName() + File.separator;
    }

    /** Constructs the absolute filename of the collection etc directory, which should resemble "$GSDLHOME/collect/&lt;col_name&gt;/etc/"
     * @return A <strong>String</strong> containing the filename.
     * @see org.greenstone.gatherer.Configuration
     * @see org.greenstone.gatherer.Gatherer
     * @see org.greenstone.gatherer.collection.Collection
     * @see org.greenstone.gatherer.util.Utility
     */
    public String getCollectionEtc() {
    return Utility.getEtcDir(Utility.getCollectionDir(Gatherer.config.gsdl_path) + collection.getName() + File.separator);
    }
    /** Constructs the absolute filename of the collection file, which should resemble "$GSDLHOME/collect/&lt;col_name&gt;/&lt;col_name&gt;.col"
     * @return A <strong>String</strong> containing the filename.
     * @see org.greenstone.gatherer.Configuration
     * @see org.greenstone.gatherer.Gatherer
     * @see org.greenstone.gatherer.collection.Collection
     * @see org.greenstone.gatherer.util.Utility
     */
    public String getCollectionFilename() {
    return Utility.getCollectionDir(Gatherer.config.gsdl_path) + collection.getName() + File.separator + collection.getName() + ".col";
    }
    /** Constructs the absolute filename of the collection images directory, which should resemble "$GSDLHOME/collect/&lt;col_name&gt;/images/"
     * @return A <strong>String</strong> containing the filename.
     * @see org.greenstone.gatherer.Configuration
     * @see org.greenstone.gatherer.Gatherer
     * @see org.greenstone.gatherer.collection.Collection
     * @see org.greenstone.gatherer.util.Utility
     */
    public String getCollectionImages() {
    return Utility.getCollectionDir(Gatherer.config.gsdl_path) + collection.getName() + File.separator + StaticStrings.IMAGES_FOLDER;
    }
    /** Constructs the absolute filename of the collection import directory, which should resemble "$GSDLHOME/collect/&lt;col_name&gt;/import/"
     * @return A <strong>String</strong> containing the filename.
     * @see org.greenstone.gatherer.Configuration
     * @see org.greenstone.gatherer.Gatherer
     * @see org.greenstone.gatherer.collection.Collection
     * @see org.greenstone.gatherer.util.Utility
     */
    public String getCollectionImport() {
    return Utility.getImportDir(Utility.getCollectionDir(Gatherer.config.gsdl_path) + collection.getName() + File.separator);
    }
    /** Constructs the absolute filename of the collection index directory, which should resemble "$GSDLHOME/collect/&lt;col_name&gt;/index/"
     * @return A <strong>String</strong> containing the filename.
     * @see org.greenstone.gatherer.Configuration
     * @see org.greenstone.gatherer.Gatherer
     * @see org.greenstone.gatherer.collection.Collection
     * @see org.greenstone.gatherer.util.Utility
     */
    public String getCollectionIndex() {
    return Utility.getIndexDir(Utility.getCollectionDir(Gatherer.config.gsdl_path) + collection.getName() + File.separator);
    }
    /** Constructs the absolute filename of the collection log directory, which should resemble "$GSDLHOME/collect/&lt;col_name&gt;/log/"
     * @return A <strong>String</strong> containing the filename.
     * @see org.greenstone.gatherer.Configuration
     * @see org.greenstone.gatherer.Gatherer
     * @see org.greenstone.gatherer.collection.Collection
     * @see org.greenstone.gatherer.util.Utility
     */
    public String getCollectionLog() {
    return Utility.getLogDir(Utility.getCollectionDir(Gatherer.config.gsdl_path) + collection.getName() + File.separator);
    }
    /** Constructs the absolute filename of the collection metadata directory, which should resemble "$GSDLHOME/collect/&lt;col_name&gt;/metadata/"
     * @return A <strong>String</strong> containing the filename.
     * @see org.greenstone.gatherer.Configuration
     * @see org.greenstone.gatherer.Gatherer
     * @see org.greenstone.gatherer.collection.Collection
     * @see org.greenstone.gatherer.util.Utility
     */
    public String getCollectionMetadata() {
    return Utility.getMetadataDir(Utility.getCollectionDir(Gatherer.config.gsdl_path) + collection.getName() + File.separator);
    }

    /** This method either returns the title of the current collection, or a placeholder string of 'No Collection'.
     * @return A <strong>String</strong> which represents what we wish to display for a collection title.
     * @see org.greenstone.gatherer.collection.Collection
     */
    /* private String getCollectionTitle() {
    if(collection != null) {
        return collection.getTitle();
    }
    return Dictionary.get("Collection.No_Collection");
    } */

    /** Retrieve the record set (tree model) associated with the current collection. */
    public TreeModel getRecordSet() {
    if(collection_model == null && collection != null) {
        // Use the import directory to generate a new FileSystemModel
        collection_model = new FileSystemModel(new FileNode(new File(getCollectionImport()), false));
        // Ensure that the manager is a change listener for the tree.
        if(fm_tree_model_listener == null) {
        fm_tree_model_listener = new FMTreeModelListener();
        }
        collection_model.addTreeModelListener(fm_tree_model_listener);
    }
    return collection_model;
    }


    static public FileNode getGreenstoneCollectionsMapping()
    {
    FileNode greenstone_collections_node = new FileNode(Dictionary.get("Tree.World"));
    greenstone_collections_node.unmap();
    return greenstone_collections_node;
    }


    static public FileNode[] getCollectionSpecificMappings()
    {
    // Return any predefined special directories
    HashMap mappings = Gatherer.config.getDirectoryMappings();
    FileNode[] mapping_nodes = new FileNode[mappings.size()];
    Iterator mappings_iterator = mappings.keySet().iterator();
    for (int i = 0; mappings_iterator.hasNext(); i++) {
        String mapping_name = (String) mappings_iterator.next();
        File mapping_file = (File) mappings.get(mapping_name);
        mapping_nodes[i] = new FileNode(mapping_file, mapping_name);
    }
    return mapping_nodes;
    }


    /** This method when called, creates a new GShell in order to run the import.pl script.
     * @see org.greenstone.gatherer.Configuration
     * @see org.greenstone.gatherer.Gatherer
     * @see org.greenstone.gatherer.gui.BuildOptions
     * @see org.greenstone.gatherer.shell.GShell
     * @see org.greenstone.gatherer.shell.GShellListener
     * @see org.greenstone.gatherer.shell.GShellProgressMonitor
     * @see org.greenstone.gatherer.util.Utility
     */
    public void importCollection() {
    importing = true;
    if(!saved()) {
        Gatherer.println("CollectionManager.importCollection().forcesave");
        import_monitor.saving();
        // Force save.
        try {
        SaveCollectionTask save_task = new SaveCollectionTask(collection);
        save_task.setImportAfter(true);
        save_task.start();
        }
        catch(Exception error) {
        Gatherer.printStackTrace(error);
        }
    }
    else {
        Gatherer.println("CollectionManager.importCollection()");
        //check that we can remove the old index before starting import
        File index_dir = new File(getCollectionIndex(), "temp.txt");
        index_dir = index_dir.getParentFile();
        if(index_dir.exists()) {
           Gatherer.println("Old Index = " + index_dir.getAbsolutePath()+", testing for deletability");
           if (!canDelete(index_dir)) {
           // tell the user
           JOptionPane.showMessageDialog(Gatherer.g_man, Dictionary.get("CollectionManager.Cannot_Delete_Index"), Dictionary.get("General.Error"), JOptionPane.ERROR_MESSAGE); 
           // tell the gui manager
           // a message for the building log 
           GShellEvent event = new GShellEvent(this, 0, GShell.IMPORT, Dictionary.get("CollectionManager.Cannot_Delete_Index_Log"), GShell.ERROR);
           Gatherer.g_man.create_pane.message(event);
           event = new GShellEvent(this, 0, GShell.IMPORT, "", GShell.ERROR);
           Gatherer.g_man.create_pane.processComplete(event);
           importing = false;
           return;
           }
           
        }

        // Remove erroneous file windows file separator as it causes problems when running import.pl
        String collection_import = getCollectionImport();
        if(collection_import.length() > 2 && collection_import.endsWith("\\")) {
        collection_import = collection_import.substring(0, collection_import.length() - 1);
        }
        String args[];
        String lang = Gatherer.config.getLanguage();
        if(Utility.isWindows()) {
        args = new String[9];
        args[0] = Gatherer.config.perl_path;
        args[1] = "-S";
        args[2] = Gatherer.config.getScriptPath() + "import.pl";
        args[3] = "-gli";
        args[4] = "-language";
        args[5] = lang;
        args[6] = "-importdir";
        args[7] = collection_import;
        args[8] = collection.getName();
        }
        else {
        args = new String[7];
        args[0] = Gatherer.config.getScriptPath() + "import.pl";
        args[1] = "-gli";
        args[2] = "-language";
        args[3] = lang;
        args[4] = "-importdir";
        args[5] = collection_import;
        args[6] = collection.getName();
        }
        collection_import = null;
        args = ArrayTools.add(args, collection.build_options.getImportValues());
        GShell shell = new GShell(args, GShell.IMPORT, BUILDING, this, import_monitor, GShell.GSHELL_IMPORT);
        shell.addGShellListener(Gatherer.g_man.create_pane);
        shell.start();
        Gatherer.println("CollectionManager.importCollection().return");
    }
    importing = false;
    }

    /** Determine if we are currently in the middle of importing (and thus, in this case, we can't allow the log writer to exit). Boy was this a mission to track down. The cascade of crap rolls out something like this: Joe Schmo clicks 'Build Collection', which calls the importCollection() method above, which in turn saves the collection with a saveTask, which fires a collectionChanged message once its finished, which drives the list of logs shown on the create pane to update, which fires a itemChanged() event to the OptionsPane who dutifully tells the current log writer thread to finish up writing (all zero lines its been asked to write) and then die. Wereapon Joe Schmo gets a pretty log to look at, but it isn't actually being written to file so the next time he tries to view it faeces hits the air motion cooling device. Joy.
     * @return true if the gli is currently importing
     */
    public boolean isImporting() {
    return importing;
    }

    /** Attempts to load the given collection. Currently uses simple serialization of the collection class.
     * @param location The path to the collection as a <strong>String</strong>.
     * @see org.greenstone.gatherer.Configuration
     * @see org.greenstone.gatherer.Gatherer
     * @see org.greenstone.gatherer.collection.Collection
     * @see org.greenstone.gatherer.msm.MetadataSetManager
     * @see org.greenstone.gatherer.msm.MSMListener
     * @see org.greenstone.gatherer.util.Utility
     */
    public boolean loadCollection(String location) {
    Gatherer.println("Load Collection '" + location + "'");
    String[] args2 = new String[1];
    args2[0] = location;
    boolean result = false;
    boolean non_gatherer_collection = false;
    // Check we have actually been given a .col file.
    if(!location.endsWith(".col")) {
        JOptionPane.showMessageDialog(Gatherer.g_man, Dictionary.get("CollectionManager.Not_Col_File", args2), Dictionary.get("General.Error"), JOptionPane.ERROR_MESSAGE);
        Gatherer.println("CollectionManager.loadCollection: Haven't been given a .col file.");
        return false;
    }
    // Check that there is the collection configuration file available

    File collection_file = new File(location);
    // Ensure that the directory exists.
    File collection_directory = collection_file.getParentFile();
    if(!collection_directory.exists()) {
        // we cant open this
        collection_directory = null;
        return false;
    }

    // Special case of a user trying to open an old greenstone collection.
    File metadata_directory = new File(collection_directory, Utility.META_DIR);
    if(!metadata_directory.exists()) {

        Gatherer.println("CollectionManager.loadCollection: trying to load up a non-gatherer collection");
        non_gatherer_collection = true;
    }

    String name = collection_directory.getName();
    File lock_file = new File(collection_file.getParentFile(), LOCK_FILE);
    // Now determine if a lock already exists on this collection.
    int choice = LockFileDialog.YES_OPTION;
    if(lock_file.exists()) {
        LockFileDialog dialog = new LockFileDialog(Gatherer.g_man, name, lock_file);
        choice = dialog.getChoice();
        dialog.dispose();
        dialog = null;
    }

    if(choice != LockFileDialog.YES_OPTION) {
        // user has cancelled
        lock_file = null;
        collection_directory = null;
        return false;
    }


    try {
        if(lock_file.exists()) {
        lock_file.delete();
        }
        // Create a lock file.
        createLockFile(lock_file);
        // This lock file may not have been created so check
        if(!lock_file.canWrite()) {
        // The lock file cannot be written to. Most likely cause incorrect file permissions.
        System.err.println("Cannot write lock file!");
        String args[] = new String[2];
        args[0] = args2[0];
        args[1] = Dictionary.get("FileActions.Write_Not_Permitted_Title");
        JOptionPane.showMessageDialog(Gatherer.g_man, Dictionary.get("CollectionManager.Cannot_Open_With_Reason", args), Dictionary.get("General.Error"), JOptionPane.ERROR_MESSAGE);
        args = null;
        return false;
        }
        // Open the collection file
        collection = new Collection(collection_file);
        if(collection.getTitle().equals(StaticStrings.ERROR_STR)) {
        collection = null;
        // Remove lock file
        if(lock_file.exists()) {
            lock_file.delete();
        }
        throw(new Exception(Dictionary.get("CollectionManager.Missing_Config")));
        }

        collection.msm = new MetadataSetManager();
        msm = collection.msm; // Legacy
        collection.msm.load();

        // if non-gatherer collection, need to add some metadata sets
        if (non_gatherer_collection) {
        if (!addSomeMetadataSets(collection_directory)) {
            // for now - return of false means its been cancelled. Any error messages should be sent from the function itself
            lock_file = null;
            collection_directory = null;
            closeCollection();
            return false;
        }
        }

        collection.cdm = new CollectionDesignManager(new File(collection_file.getParent(), Utility.CONFIG_DIR));
        if (non_gatherer_collection) {
        // We first recurse the Import folder tree, reading in any metadata.xml files, and then altering the non-namespaced element names to be valid GLI names
        LegacyCollectionImporter lci = new LegacyCollectionImporter(collection_directory, collection.cdm);
        lci.importMetadata();
        lci.updateClassifiers();
        lci = null;
        }

        // Whether the collection is legacy or not, we should now be able to prepare the MetadataXMLFileManager
        collection.gdm = new MetadataXMLFileManager();

        // Tell everyone that it worked.
        String[] args = new String[1];
        args[0] = name;
        Gatherer.println(Dictionary.get("CollectionManager.Loading_Successful", args));
        // Now we need to hook up classes that depend on messages from the metadata set manager to keep their content fresh.
        collection.msm.addMSMListener(this);
        // We're done. Let everyone know.
        if(Gatherer.g_man != null) {
        // workspace_model = null;
        Gatherer.g_man.collectionChanged(ready());
        }
        result = true;
        ///ystem.err.println("Done loadCollection().");
    } catch (Exception error) {
        System.err.println("Exception occurred!");
        error.printStackTrace();
        // There is obviously no existing collection present.
        Gatherer.printStackTrace(error);
        if(error.getMessage() != null) {
        String[] args = new String[2];
        args[0] = args2[0];
        args[1] = error.getMessage();
        JOptionPane.showMessageDialog(Gatherer.g_man, Dictionary.get("CollectionManager.Cannot_Open_With_Reason", args), Dictionary.get("General.Error"), JOptionPane.ERROR_MESSAGE);
        }
        else {
        JOptionPane.showMessageDialog(Gatherer.g_man, Dictionary.get("CollectionManager.Cannot_Open", args2), Dictionary.get("General.Error"), JOptionPane.ERROR_MESSAGE);
        }
    }

    lock_file = null;
    collection_directory = null;

    args2 = null;
    return result;
    }

    /** I started giving the user the choice of using an existing meta set or creating a new one. The second option being so that they didn't have to add/merge/ignore each element, they could all be added automatically. However, I am not sure where the merge prompt gets called from, and it is not essential, so I am leaving it for now - it shoudl be added back in and finished. [kjdon] */
    private boolean addSomeMetadataSets(File collection_dir) {


    ExternalCollectionPrompt external_prompt = new ExternalCollectionPrompt();
    int meta_choice = external_prompt.getMetadataChoice();
    boolean cancelled = external_prompt.isCancelled();
    if (cancelled) {
        return false;
    }

    /*if (meta_choice == ExternalCollectionPrompt.NEW_META_SET) {
        NewMetaSetPrompt nmsp = new NewMetaSetPrompt();
        if (nmsp.isCancelled()) {
        return false;
}
        String namespace_str = nmsp.getNamespace();
        String name_str = nmsp.getName();
        MetadataSet set = Gatherer.c_man.msm.addSet(namespace_str, name_str);
    } else if (meta_choice == ExternalCollectionPrompt.EXISTING_META_SET) {
    */
    // now we reuse the newcoll metadata prompt for the user to select metadata sets
    NewCollectionMetadataPrompt ncm_prompt = new NewCollectionMetadataPrompt(true);
    if (ncm_prompt.isCancelled()) {
        return false;
    }
    ArrayList metadata_sets = ncm_prompt.getSets();
    // Import default metadata sets if any.
    for(int i = 0; metadata_sets != null && i < metadata_sets.size(); i++) {
        MetadataSet metadata_set = (MetadataSet) metadata_sets.get(i);
        collection.msm.importMDS(metadata_set.getFile(), false);
    }
    /*} else {
      return false;
      }*/
    // Always import the extracted metadata set
    collection.msm.importMDS(new File(Utility.METADATA_DIR + Utility.EXTRACTED_METADATA_NAMESPACE + StaticStrings.METADATA_SET_EXTENSION), false);

    return true;
    }

    private boolean searchForMetadata(TreeModel collection_tree, FileNode current_node) {
    File source_file = current_node.getFile();
    String source_file_name = source_file.getName();
    if (source_file_name.equals(Utility.METADATA_XML) || source_file_name.equals("CVS")) {
        return true;
    }
    if (collection.msm.searchForMetadata(current_node, current_node, false)== false) {
        return false;
    }
    int num_children = collection_tree.getChildCount(current_node);
    for (int i=0; i<num_children; i++) {
        FileNode child = (FileNode)collection_tree.getChild(current_node, i);
        if (searchForMetadata(collection_tree, child)==false) {
        return false;
        }
    }
    return true;
    }

    public void makeCollection(String description, String email, String name, String title) {
    // Encode the description so it is safe to write to shell
    if(Utility.isWindows()) {
        description = Codec.transform(description, Codec.TEXT_TO_SHELL_WINDOWS);
    }
    else {
        description = Codec.transform(description, Codec.TEXT_TO_SHELL_UNIX);
    }
    // Run the mkcol command.
    String command[];
    if(Utility.isWindows()) {
        if(description == null || title == null) {
        command = new String[4];
        command[0] = Gatherer.config.perl_path;
        command[1] = "-S";
        command[2] = Gatherer.config.getScriptPath() + "mkcol.pl";
        command[3] = name;
        }
        // Users are no longer required to supply an email
        else if(email == null) {
        command = new String[8];
        command[0] = Gatherer.config.perl_path;
        command[1] = "-S";
        command[2] = Gatherer.config.getScriptPath() + "mkcol.pl";
        command[3] = "-title";
        command[4] = title;
        command[5] = "-about";
        command[6] = description;
        command[7] = name;
        }
        else {
        command = new String[10];
        command[0] = Gatherer.config.perl_path;
        command[1] = "-S";
        command[2] = Gatherer.config.getScriptPath() + "mkcol.pl";
        command[3] = "-title";
        command[4] = title;
        command[5] = "-creator";
        command[6] = email;
        command[7] = "-about";
        command[8] = description;
        command[9] = name;
        }
    }
    else {
        if(description == null || title == null) {
        command = new String[2];
        command[0] = "mkcol.pl";
        command[1] = name;
        }
        else if(email == null) {
        command = new String[6];
        command[0] = "mkcol.pl";
        command[1] = "-title";
        command[2] = title;
        command[3] = "-about";
        command[4] = description;
        command[5] = name;
        }
        else {
        command = new String[8];
        command[0] = "mkcol.pl";
        command[1] = "-title";
        command[2] = title;
        command[3] = "-creator";
        command[4] = email;
        command[5] = "-about";
        command[6] = description;
        command[7] = name;
        }
    }
    GShell process = new GShell(command, GShell.NEW, COLLECT, this, null, GShell.GSHELL_NEW);
    process.addGShellListener(this);
    process.run(); // Don't bother threading this... yet
    }

    /** Any implementation of GShellListener must include this method to allow the GShell to send messages to listeners. However in this case the CollectionManager is in no way interested in what the messages are, just the import events which have a specific type and are handled elsewhere. Thus we can safely ignore this event.
     * @param event A <strong>GShellEvent</strong> which contains a the message.
     */
    public synchronized void message(GShellEvent event) {
    }
    /** Called whenever the metadata value changes in some way, such as the addition of a new value. We want to mark the collection so that it needs saving again.
     * @param event A <strong>MSMEvent</strong> containing details of the event that caused this message to be fired.
     * @see org.greenstone.gatherer.collection.Collection
     */
    public void metadataChanged(MSMEvent event) {
    // Again this change means we need to save the collection again.
    collection.setSaved(false);
    }
    /** This call is fired whenever a process within a GShell created by this class begins.
     * @param event A <strong>GShellEvent</strong> containing information about the GShell process.
     * @see org.greenstone.gatherer.Gatherer
     * @see org.greenstone.gatherer.gui.GUIManager
     * @see org.greenstone.gatherer.shell.GShell
     */
    public synchronized void processBegun(GShellEvent event) {
    Gatherer.println("CollectionManager.processBegun(" + event.getType() + ")");
    ///ystem.err.println("ProcessBegun " + event.getType());
    // If this is one of the types where we wish to lock user control
    Gatherer.g_man.lockCollection((event.getType() == GShell.IMPORT), true);
    }
    /** This call is fired whenever a process within a GShell created by this class ends.
     * @param event A <strong>GShellEvent</strong> containing information about the GShell process.
     * @see org.greenstone.gatherer.Gatherer
     * @see org.greenstone.gatherer.gui.GUIManager
     * @see org.greenstone.gatherer.shell.GShell
     */
    public synchronized void processComplete(GShellEvent event) {
    Gatherer.println("CollectionManager.processComplete(" + event.getType() + ")");
    ///ystem.err.println("ProcessComplete " + event.getType());
    Gatherer.g_man.lockCollection((event.getType() == GShell.IMPORT), false);
    ///ystem.err.println("Recieved process complete event - " + event);
    // If we were running an import, now run a build.
    if(event.getType() == GShell.IMPORT && event.getStatus() == GShell.OK) {
        // Finish import.
        collection.setImported(true);
        buildCollection();
    }
    // If we were running a build, now is when we move files across.
    else if(event.getType() == GShell.BUILD && event.getStatus() == GShell.OK) {
        if(installCollection()) {
        // If we have a local library running (that we know about) then we ask it to add our newly create collection
        if(Gatherer.config.exec_file != null) {
            Gatherer.self.configServer(GSDLSiteConfig.ADD_COMMAND + collection.getName());
        }

        // Fire a collection changed first to update the preview etc buttons
        Gatherer.g_man.collectionChanged(ready());

        // Now display a message dialog saying its all built
        WarningDialog collection_built_warning_dialog = new WarningDialog("warning.CollectionBuilt", false);
        collection_built_warning_dialog.setMessageOnly(true); // Not a warning
        collection_built_warning_dialog.display();
        collection_built_warning_dialog.dispose();
        collection_built_warning_dialog = null;
        }
        else {
        JOptionPane.showMessageDialog(Gatherer.g_man, Dictionary.get("CollectionManager.Preview_Ready_Failed"), Dictionary.get("CollectionManager.Preview_Ready_Title"), JOptionPane.ERROR_MESSAGE);
        Gatherer.g_man.collectionChanged(ready());
        }
    }
    else if(event.getStatus() == GShell.ERROR || event.getStatus() == GShell.CANCELLED) {
        JOptionPane.showMessageDialog(Gatherer.g_man, Dictionary.get("CollectionManager.Preview_Ready_Failed"), Dictionary.get("CollectionManager.Preview_Ready_Title"), JOptionPane.ERROR_MESSAGE);
        Gatherer.g_man.collectionChanged(ready());
        Gatherer.g_man.repaint(); // It appears Java's own dialogs have the same not always painting correct area bug that I suffer from. Well I don't suffer from it personally, but my ModalDialog components do.
    }
    }
    /** Determine if the manager is ready for actions apon its collection.
     * @return A <i>boolean</i> which is <i>true</i> to indicate a collection has been loaded and thus the collection is ready for editing, <i>false</i> otherwise.
     */
    static public synchronized boolean ready() {
    if(collection != null) {
        return true;
    }
    else {
        return false;
    }
    }

    public synchronized boolean reallyReady() {
    // If the closing thread is non-null we should only allow that thread to see the collection as closed.
    if(closing_thread != null) {
        // Only the closing thread sees the truth
        if(Thread.currentThread() == closing_thread) {
        return (collection == null);
        }
        // All other threads are told a lie.
        else {
        return true;
        }
    }
    else {
        if(collection != null) {
        return true;
        }
        else {
        return false;
        }
    }
    }

    /** This method associates the collection build monitor with the build monitor created in CreatePane.
     * @param monitor A <strong>GShellProgressMonitor</strong> which we will use as the build monitor.
     */
    public void registerBuildMonitor(GShellProgressMonitor monitor) {
    build_monitor = monitor;
    }
    /** This method associates the collection import monitor with the import monitor created in CreatePane.
     * @param monitor A <strong>GShellProgressMonitor</strong> which we will use as the import monitor.
     */
    public void registerImportMonitor(GShellProgressMonitor monitor) {
    import_monitor = monitor;
    }
    /** Remove a previously assigned special directory mapping.
     * @param target The <string>FileNode</strong> representing the special directory mapping to remove as a <strong>String</strong>.
     * @return The <strong>File</strong> of the mapping removed.
     * @see org.greenstone.gatherer.file.FileNode
     */
    public File removeDirectoryMapping(FileNode target) {
    // Remove from config, remembering file
    File file = Gatherer.config.removeDirectoryMapping(target.toString());
    // Update tree.
    Gatherer.g_man.gather_pane.refreshWorkspaceTree(WorkspaceTree.MAPPED_DIRECTORIES_CHANGED);
    return file;
    }
    /** Used to check whether all open collections have a 'saved' state.
     * @return A <i>boolean</i> which is <i>true</i> if the collection has been saved.
     * @see org.greenstone.gatherer.collection.Collection
     */
    public boolean saved() {
    boolean result = true;
    if(collection != null) {
        result = collection.getSaved();
    }
    return result;
    }
    /** Saves a collection by serializing it to file.
     * @param close_after <i>true</i> to cause the Gatherer to close the collection once save is complete, <i>false</i> otherwise.
     * @param exit_after <i>true</i> to cause the Gatherer to exit once save is complete, <i>false</i> otherwise.
     * @see org.greenstone.gatherer.Gatherer
     * @see org.greenstone.gatherer.gui.GUIManager
     * @see org.greenstone.gatherer.collection.Collection
     */
    public void saveCollection(boolean close_after, boolean exit_after) {
    Gatherer.println("Save collection: " + collection.getName());
    try {
        SaveCollectionTask save_task = new SaveCollectionTask(collection, close_after, exit_after);
        save_task.start();
        // Run this in the same thread
        //save_task.run();
    }
    catch(Exception error) {
        Gatherer.printStackTrace(error);
    }
    }
    /** Saves the current collection to a new filename, then restores the original collection. Finally opens the collection copy.
     * @param name The name collection name.
     */
    public void saveCollectionAs(String name) {
    // We need to do this in a separate thread so create a SaveCollectionAsTask
    try {
        SaveCollectionTask save_task = new SaveCollectionTask(collection, name);
        save_task.start();
    }
    catch(Exception error) {
        Gatherer.printStackTrace(error);
    }
    }

    /** Method that is called whenever the metadata set collection changes in some way, such as the addition of a new set or the merging of two sets. We want to mark the collection so that it needs saving again.
     * @param event A <strong>MSMEvent</strong> containing details of the event that caused this message to be fired.
     * @see org.greenstone.gatherer.collection.Collection
     */
    public void setChanged(MSMEvent event) {
    // Invalidate saved
    collection.setSaved(false);
    }

    public void setClosingThread(boolean set) {
    if(set) {
        closing_thread = Thread.currentThread();
    }
    else {
        closing_thread = null;
    }
    }

    /** Updates the given workspace tree model to reference the private cache of the currently loaded collection. */
    /* private void updatePrivateWorkspace(DefaultTreeModel model) {
    // Add Private workspace if a collection has been loaded.
    if(ready() && !Gatherer.config.get("workflow.mirror", true)) {
        FileNode root = (FileNode)model.getRoot();
                // Remove old private workspace
        FileNode old = (FileNode)model.getChild(root, 2);
        model.removeNodeFromParent(old);
                // Create and insert new.
        FileNode private_workspace = new FileNode(new File(getCollectionCache()), Dictionary.get("Tree.Private"));
        model.insertNodeInto(private_workspace, root, 2);
    }
    } */
    /** Called whenever the value tree of an metadata element changes in some way, such as the addition of a new value. We want to mark the collection so that it needs saving again.
     * @param event A <strong>MSMEvent</strong> containing details of the event that caused this message to be fired.
     * @see org.greenstone.gatherer.collection.Collection
     */
    public void valueChanged(MSMEvent event) {
    collection.setSaved(false);
    }

    /** Install collection by moving its files from building to index after a successful build.
     * @see org.greenstone.gatherer.Gatherer
     * @see org.greenstone.gatherer.util.Utility
     */
    private boolean installCollection() {
    Gatherer.println("Build complete. Moving files.");

    try {
        // We have to ensure that the local library
        if(Gatherer.config.exec_file != null) {
        ///ystem.err.println("Local Library Found!");
        //Gatherer.g_man./review_pane.configServer(GSDLSiteConfig.RELEASE_COMMAND + collection.getName());
        Gatherer.self.configServer(GSDLSiteConfig.RELEASE_COMMAND + collection.getName());
        }

        File index_dir = new File(getCollectionIndex(), "temp.txt");
        index_dir = index_dir.getParentFile();
        if(index_dir.exists()) {
           Gatherer.println("Index = " + index_dir.getAbsolutePath());
        }

        File build_dir = new File(getCollectionBuild(), "temp.txt");
        build_dir = build_dir.getParentFile();
        Gatherer.println("Build = " + build_dir.getAbsolutePath());

        // Get the build mode from the build options
        String build_mode = collection.build_options.getBuildValue("mode");

        // Special case for build mode "all": replace index dir with building dir
        if (build_mode == null || build_mode.equals(Dictionary.get("CreatePane.Mode_All"))) {
        // Remove the old index directory
        if (index_dir.exists()) {
            Utility.delete(index_dir);
            // Check the delete worked
            if (index_dir.exists()) {
            throw new Exception("Index directory cannot be removed.");
            }
        }

        // Move the building directory to become the new index directory
        if (build_dir.renameTo(index_dir) == false) {
            throw new Exception("Build directory cannot be moved.");
        }

        // Create a new building directory
        File new_build = new File(getCollectionBuild(), "temp.txt");
        new_build = new_build.getParentFile();
        new_build.mkdir();
        }

        // Otherwise copy everything in the building dir into the index dir
        else {
        File[] build_files = build_dir.listFiles();
        for (int i = 0; i < build_files.length; i++) {
            File build_file = build_files[i];
            File index_equivalent = new File(index_dir, build_file.getName());

            // Remove the old file in the index directory (if it exists)
            if (index_equivalent.exists()) {
            Utility.delete(index_equivalent);
            // Check the delete worked
            if (index_equivalent.exists()) {
                throw new Exception("Index file " + index_equivalent + " cannot be removed.");
            }
            }

            // Move the file into the index directory
            if (build_file.renameTo(index_equivalent) == false) {
            throw new Exception("File " + build_file + " cannot be moved into index directory.");
            }
        }
        }
    }
    catch (Exception exception) {
        JOptionPane.showMessageDialog(Gatherer.g_man, "Exception detected during collection install.\nMost likely caused by Windows or Local Library holding locks on files:\n" + exception.getMessage(), "Error", JOptionPane.ERROR_MESSAGE);
        return false;
    }
    return true;
    }

    private boolean searchArchivesForMetadata(File archive_directory) {
    /** @todo - ensure GreenstoneArchiveParser works as expected. */
    return true;
    }

    /** now this returns true if successful, false if unsuccessful or cancelled */
    private boolean searchForMetadata(File current_file) {
    boolean success = true;
       if(current_file.isFile() && current_file.getName().equals(Utility.METADATA_XML)) {
           success = collection.msm.searchForMetadata(null, new FileNode(current_file), false, true); // A dummy run only.
       }
       else {
           File[] children_files = current_file.listFiles();
           for(int i = 0; success && children_files != null && i < children_files.length; i++) {
               success = searchForMetadata(children_files[i]);
           }
       }
       return success;
     }
    
    private void updateCollectionCFG(File base_cfg, File new_cfg, String description, String email, String title) {
    boolean first_name = true;
    boolean first_extra = true;
    String collection_path = (base_cfg.getParentFile().getParentFile()).getAbsolutePath();
    
    HashMap mappings = collection.msm.profiler.getActions(collection_path);
    if(mappings == null) {
        Gatherer.println("Mappings is null, which is odd. Leaving all configuration commands which use metadata as they are.");
    }
    
    // Now read in base_cfg line by line, parsing important onces and/or replacing them with information pertinent to our collection. Each line is then written back out to the new collect.cfg file.
    try {
        BufferedReader in = new BufferedReader(new InputStreamReader(new FileInputStream(base_cfg), "UTF-8"));
        BufferedWriter out = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(new_cfg), "UTF-8"));
        String command = null;
        while((command = in.readLine()) != null) {
        // We have to test the end of command for the special character '\'. If found, remove it and append the next line, then repeat.
        while(command.trim().endsWith("\\")) {
            command = command.substring(0, command.lastIndexOf("\\"));
            String next_line = in.readLine();
            if(next_line != null) {
            command = command + next_line;
            }
        }
        ///ystem.err.println("Read: " + command);
        // Now we've finished parsing a line, determine what to do with it.
        String command_lc = command.toLowerCase();
        if (command_lc.startsWith(StaticStrings.COLLECTIONMETADATA_STR)) {
            // we don't want to import collectionname, collectionextra, iconcollection, iconcollectionsmall from the base collection
            StringTokenizer tokeniser = new StringTokenizer(command_lc);
            tokeniser.nextToken(); // remove the first one
            String meta_name = tokeniser.nextToken();
            tokeniser = null;
            if (meta_name.equals(StaticStrings.COLLECTIONMETADATA_COLLECTIONNAME_STR) || meta_name.equals(StaticStrings.COLLECTIONMETADATA_COLLECTIONEXTRA_STR) || meta_name.equals(StaticStrings.COLLECTIONMETADATA_ICONCOLLECTION_STR) || meta_name.equals(StaticStrings.COLLECTIONMETADATA_ICONCOLLECTIONSMALL_STR) ) {
            continue;
            }
        }
        // Just before we try more general parsing there are the special cases to check. These are explicit changes required by some collections to produce sensible results.
        if(command_lc.startsWith(Utility.CFG_CLASSIFY)) {
            StringTokenizer tokenizer = new StringTokenizer(command);
            StringBuffer text = new StringBuffer(tokenizer.nextToken());
            // Read in the classifier command watching for hfile, metadata and sort arguments.
            String buttonname = null;
            String hfile = null;
            String new_metadata = null;
            String old_metadata = null;
            while(tokenizer.hasMoreTokens()) {
            String token = tokenizer.nextToken();
            if(token.equals(Utility.CFG_CLASSIFY_HFILE)) {
                if(tokenizer.hasMoreTokens()) {
                text.append(" ");
                text.append(token);
                token = tokenizer.nextToken();
                hfile = token;
                }
            }
            else if(token.equals(Utility.CFG_CLASSIFY_METADATA)) {
                if(tokenizer.hasMoreTokens()) {
                text.append(" ");
                text.append(token);
                String temp_metadata = tokenizer.nextToken();
                String replacement = null;
                if(mappings != null) {
                    replacement = (String) mappings.get(temp_metadata);
                }
                if(replacement != null) {
                    token = replacement;
                    old_metadata = temp_metadata;
                    new_metadata = replacement;
                }
                else {
                    token = temp_metadata;
                }
                temp_metadata = null;
                replacement = null;
                }
            }
            else if(token.equals(Utility.CFG_CLASSIFY_SORT)) {
                if(tokenizer.hasMoreTokens()) {
                text.append(" ");
                text.append(token);
                String temp_metadata = tokenizer.nextToken();
                String replacement = null;
                if(mappings != null) {
                    replacement = (String) mappings.get(temp_metadata);
                }
                if(replacement != null) {
                    token = replacement;
                }
                else {
                    token = temp_metadata;
                }
                temp_metadata = null;
                replacement = null;
                }
            }
            else if(token.equals(Utility.CFG_CLASSIFY_BUTTONNAME)) {
                buttonname = token;
            }
            text.append(' ');
            text.append(token);
            token = null;
            }
            tokenizer = null;
            
            // If we replaced the metadata argument and didn't encounter a buttonname, then add one now pointing back to the old metadata name in order to accomodate macro files which required such names (buttonname is metadata name by default)!
            if(old_metadata != null && new_metadata != null && buttonname == null) {
            text.append(' ');
            text.append(Utility.CFG_CLASSIFY_BUTTONNAME);
            text.append(' ');
            text.append(old_metadata);
            }
            command = text.toString();
            // Replace the hfile if we found it
            if(hfile != null && new_metadata != null) {
            command = command.replaceAll(hfile, new_metadata + ".txt");
            }
            buttonname = null;
            hfile = null;
            new_metadata = null;
            old_metadata = null;
            write(out, command);
        }
        else {
            // There is still one special case, that of the format command. In such a command we have to search for [<target>] to ensure we don't change parts of the format which have nothing to do with the metadata elements.
            boolean format_command = command_lc.startsWith(Utility.CFG_FORMAT);
            // Replace mapping strings
            if(mappings != null) {
            for(Iterator keys = mappings.keySet().iterator(); keys.hasNext(); ) {
                String target = (String) keys.next();
                String replacement = (String) mappings.get(target);
                if(format_command) {
                target = "\\[" + target + "\\]";
                replacement = "{Or}{[" + replacement + "]," + target + "}";
                }
                command = command.replaceAll(target, replacement);
            }
            }
            write(out, command);
        }
        }
        in.close();
        in = null;
        out.flush();
        out.close();
        out = null;
    }
    catch(Exception error) {
        Gatherer.printStackTrace(error);
    }
    // All done, I hope.
    }
    
    private void write(BufferedWriter out, String message)
    throws Exception {
    ///ystem.err.println("Writing: " + message);
    out.write(message, 0, message.length());
    out.newLine();
    }

    /** The CollectionManager class is getting too confusing by half so I'll implement this TreeModelListener in a private class to make responsibility clear. */
    private class FMTreeModelListener
    implements TreeModelListener {
    /** Any action that changes one of the tree models within a collection, which are the only models we listen to, mean the collections contents have changed and so saved should be set to false.
     * @param event A <strong>TreeModelEvent</strong> encompassing all the information about the event which has changed the tree.
     */
    public void treeNodesChanged(TreeModelEvent event) {
        if(collection != null) {
        collection.setSaved(false);
        }
    }
    /** Any action that changes one of the tree models within a collection, which are the only models we listen to, mean the collections contents have changed and so saved should be set to false.
     * @param event A <strong>TreeModelEvent</strong> encompassing all the information about the event which has changed the tree.
     */
    public void treeNodesInserted(TreeModelEvent event) {
        if(collection != null) {
        collection.setSaved(false);
        }
    }
    /** Any action that changes one of the tree models within a collection, which are the only models we listen to, mean the collections contents have changed and so saved should be set to false.
     * @param event A <strong>TreeModelEvent</strong> encompassing all the information about the event which has changed the tree.
     */
    public void treeNodesRemoved(TreeModelEvent event) {
        if(collection != null) {
        collection.setSaved(false);
        }
    }
    /** Any action that changes one of the tree models within a collection, which are the only models we listen to, mean the collections contents have changed and so saved should be set to false.
     * @param event A <strong>TreeModelEvent</strong> encompassing all the information about the event which has changed the tree.
     */
    public void treeStructureChanged(TreeModelEvent event) {
        if(collection != null) {
        collection.setSaved(false);
        }
    }
    }
}