source: main/trunk/greenstone3/src/java/org/greenstone/gsdl3/service/GS2Construct.java@ 33051

/*
 *    GS2Construct.java 
 *    Copyright (C) 2002 New Zealand Digital Library, http://www.nzdl.org
 *
 *    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.gsdl3.service;

import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.Serializable;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.Collections;
import java.util.Iterator;
import java.util.Map.Entry;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import org.apache.log4j.Logger;
import org.greenstone.gsdl3.build.GS2PerlConstructor;
import org.greenstone.gsdl3.build.GS2PerlListener;
import org.greenstone.gsdl3.util.GSFile;
import org.greenstone.gsdl3.util.GSParams;
import org.greenstone.gsdl3.util.GSPath;
import org.greenstone.gsdl3.util.GSStatus;
import org.greenstone.gsdl3.util.GSXML;
import org.greenstone.gsdl3.util.OID;
import org.greenstone.gsdl3.util.SimpleCollectionDatabase;
import org.greenstone.gsdl3.util.UserContext;
import org.greenstone.gsdl3.util.XMLConverter;

// https://developer.android.com/reference/org/json/JSONObject.html
// https://developer.android.com/reference/org/json/JSONArray.html
import org.json.JSONArray;
import org.json.JSONException;
import org.json.JSONObject;


import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.Text;

/**
 * A Services class for building collections provides a wrapper around the old
 * perl scripts
 * 
 * @author Katherine Don
 */
public class GS2Construct extends ServiceRack
{

    static Logger logger = Logger.getLogger(org.greenstone.gsdl3.service.GS2Construct.class.getName());

    // default error message
    private static final String NO_PERMISSIONS_ERROR = "This user does not have the required permissions to perform this action.";

    // services offered
    private static final String NEW_SERVICE = "NewCollection";
    private static final String ADD_DOC_SERVICE = "AddDocument";
    private static final String IMPORT_SERVICE = "ImportCollection";
    private static final String BUILD_SERVICE = "BuildCollection";
    private static final String ACTIVATE_SERVICE = "ActivateCollection";
    private static final String BUILD_AND_ACTIVATE_SERVICE = "BuildAndActivateCollection";
    private static final String DELETE_SERVICE = "DeleteCollection";
    private static final String RELOAD_SERVICE = "ReloadCollection";
    private static final String MODIFY_METADATA_SERVICE = "ModifyMetadata"; // set or remove metadata


    // params used
    private static final String COL_PARAM = "collection";
    private static final String NEW_COL_TITLE_PARAM = "collTitle";
    private static final String NEW_COL_ABOUT_PARAM = "collAbout";
    private static final String CREATOR_PARAM = "creator";
    private static final String NEW_FILE_PARAM = "newfile";
    private static final String PROCESS_ID_PARAM = GSParams.PROCESS_ID;
    private static final String BUILDTYPE_PARAM = "buildType";
    private static final String BUILDTYPE_MG = "mg";
    private static final String BUILDTYPE_MGPP = "mgpp";

    protected static String DATABASE_TYPE = null;
    protected SimpleCollectionDatabase coll_db = null;
    
    // the list of the collections - store between some method calls
    private String[] collection_list = null;

    // set of listeners for any construction commands
    protected Map<String, GS2PerlListener> listeners = null;
    protected HashMap<String, Boolean> collectionOperationMap = new HashMap<String, Boolean>();

    public GS2Construct()
    {
        this.listeners = Collections.synchronizedMap(new HashMap<String, GS2PerlListener>());
    }

  // in configure we set up any params that should be saved to the session. At this stage, assuming none should be saved.
  
    /** returns a specific service description */
    protected Element getServiceDescription(Document doc, String service, String lang, String subset)
    {

        Element description = doc.createElement(GSXML.SERVICE_ELEM);
        description.setAttribute(GSXML.TYPE_ATT, GSXML.SERVICE_TYPE_PROCESS);
        description.setAttribute(GSXML.NAME_ATT, service);
        if (subset == null || subset.equals(GSXML.DISPLAY_TEXT_ELEM + GSXML.LIST_MODIFIER))
        {
            description.appendChild(GSXML.createDisplayTextElement(doc, GSXML.DISPLAY_TEXT_NAME, getTextString(service + ".name", lang)));
            description.appendChild(GSXML.createDisplayTextElement(doc, GSXML.DISPLAY_TEXT_DESCRIPTION, getTextString(service + ".description", lang)));
            description.appendChild(GSXML.createDisplayTextElement(doc, GSXML.DISPLAY_TEXT_SUBMIT, getTextString(service + ".submit", lang)));
        }
        if (subset == null || subset.equals(GSXML.PARAM_ELEM + GSXML.LIST_MODIFIER))
        {
            Element param_list = doc.createElement(GSXML.PARAM_ELEM + GSXML.LIST_MODIFIER);
            description.appendChild(param_list);

            if (service.equals(NEW_SERVICE))
            {

                Element param = GSXML.createParameterDescription(doc, NEW_COL_TITLE_PARAM, getTextString("param." + NEW_COL_TITLE_PARAM, lang), GSXML.PARAM_TYPE_STRING, null, null, null);
                param_list.appendChild(param);
                param = GSXML.createParameterDescription(doc, CREATOR_PARAM, getTextString("param." + CREATOR_PARAM, lang), GSXML.PARAM_TYPE_STRING, null, null, null);
                param_list.appendChild(param);
                param = GSXML.createParameterDescription(doc, NEW_COL_ABOUT_PARAM, getTextString("param." + NEW_COL_ABOUT_PARAM, lang), GSXML.PARAM_TYPE_TEXT, null, null, null);
                param_list.appendChild(param);
                String[] types = { BUILDTYPE_MGPP, BUILDTYPE_MG };
                String[] type_texts = { getTextString("param." + BUILDTYPE_PARAM + "." + BUILDTYPE_MGPP, lang), getTextString("param." + BUILDTYPE_PARAM + "." + BUILDTYPE_MG, lang) };

                param = GSXML.createParameterDescription(doc, BUILDTYPE_PARAM, getTextString("param." + BUILDTYPE_PARAM, lang), GSXML.PARAM_TYPE_ENUM_SINGLE, BUILDTYPE_MGPP, types, type_texts);
                param_list.appendChild(param);
            }
            else if (service.equals(ACTIVATE_SERVICE) || service.equals(IMPORT_SERVICE) || service.equals(BUILD_SERVICE) || service.equals(RELOAD_SERVICE) || service.equals(DELETE_SERVICE) || service.equals(MODIFY_METADATA_SERVICE))
            {

                this.collection_list = getCollectionList();
                Element param = GSXML.createParameterDescription(doc, COL_PARAM, getTextString("param." + COL_PARAM, lang), GSXML.PARAM_TYPE_ENUM_SINGLE, null, this.collection_list, this.collection_list);
                param_list.appendChild(param);
            }
            else
            {
                // invalid service name
                return null;
            }
        }
        return description;
    }

    // each service must have a method "process<New service name>"

    protected Element processNewCollection(Element request)
    {
        if (!userHasCollectionEditPermissions(request)) {
        return errorResponse("processNewCollection", NO_PERMISSIONS_ERROR);
        }
        return runCommand(request, GS2PerlConstructor.NEW);
    }

    /** TODO:implement this */
    protected Element processAddDocument(Element request)
    {
        if (!userHasCollectionEditPermissions(request)) {
        return errorResponse("processAddDocument", NO_PERMISSIONS_ERROR);
        }

      Document result_doc = XMLConverter.newDOM();
        // decode the file name, add it to the import directory
        String name = GSPath.getFirstLink(request.getAttribute(GSXML.TO_ATT));
        Element response = result_doc.createElement(GSXML.RESPONSE_ELEM);
        response.setAttribute(GSXML.FROM_ATT, name);
        Element status = result_doc.createElement(GSXML.STATUS_ELEM);
        response.appendChild(status);
        //String lang = request.getAttribute(GSXML.LANG_ATT);
        //String request_type = request.getAttribute(GSXML.TYPE_ATT);
        Text t = result_doc.createTextNode("AddDocument: not implemented yet");
        status.appendChild(t);
        status.setAttribute(GSXML.STATUS_ERROR_CODE_ATT, Integer.toString(GSStatus.ERROR));
        return response;
    }

    protected Element processBuildAndActivateCollection(Element request)
    {
        // check permissions
        if (!userHasCollectionEditPermissions(request)) {
        return errorResponse("processBuildAndActivateCollection", NO_PERMISSIONS_ERROR);
        }

            
        waitUntilReady(request);
        Element buildResponse = processBuildCollection(request);
        if (buildResponse.getElementsByTagName(GSXML.ERROR_ELEM).getLength() > 0)
        {
            signalReady(request);
            return buildResponse;
        }

        Element statusElem = (Element) buildResponse.getElementsByTagName(GSXML.STATUS_ELEM).item(0);
        String id = statusElem.getAttribute("pid");

        GS2PerlListener currentListener = this.listeners.get(id);
        int statusCode = currentListener.getStatus();
        while (!GSStatus.isCompleted(statusCode))
        {
            // wait for the process, and keep checking the status code
            // there is probably a better way to do this.
            try
            {
                Thread.currentThread().sleep(100);
            }
            catch (Exception e)
            { // ignore
            }
            statusCode = currentListener.getStatus();
        }

        Element activateResponse = processActivateCollection(request);
        signalReady(request);
        return activateResponse;
    }

    protected Element processImportCollection(Element request)
    {
        if (!userHasCollectionEditPermissions(request)) {
        return errorResponse("processImportCollection", NO_PERMISSIONS_ERROR);
        }

        Element param_list = (Element) GSXML.getChildByTagName(request, GSXML.PARAM_ELEM + GSXML.LIST_MODIFIER);
        HashMap<String, Serializable> params = GSXML.extractParams(param_list, false);

        if (params == null)
        {
            return null;
        }

        //If we have been requested to only build certain documents then we need to create a manifest file
        String documentsParam = (String) params.get("documents");
        if (documentsParam != null && !documentsParam.equals(""))
        {
            String s = File.separator;
            String manifestFolderPath = this.site_home + s + "collect" + s + params.get(COL_PARAM) + s + "manifests";
            String manifestFilePath = manifestFolderPath + File.separator + "tempManifest.xml";

            File manifestFolderFile = new File(manifestFolderPath);
            if (!manifestFolderFile.exists())
            {
                manifestFolderFile.mkdirs();
            }

            File manifestFile = new File(manifestFilePath);
            if (!manifestFile.exists())
            {
                try
                {
                    manifestFile.createNewFile();
                }
                catch (Exception ex)
                {
                    ex.printStackTrace();
                    return null; //Probably should return an actual error
                }
            }
            String[] docList = documentsParam.split(",");

            try
            {
                BufferedWriter bw = new BufferedWriter(new FileWriter(manifestFile));
                bw.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
                bw.write("<Manifest>\n");
                bw.write("  <Index>\n");
                for (int j = 0; j < docList.length; j++)
                {
                    bw.write("    <Filename>" + docList[j] + "</Filename>\n");
                }
                bw.write("  </Index>\n");
                bw.write("</Manifest>\n");
                bw.close();
            }
            catch (Exception ex)
            {
                ex.printStackTrace();
                return null; //Probably should return an actual error
            }
        }

        return runCommand(request, GS2PerlConstructor.IMPORT);
    }

    protected Element processBuildCollection(Element request)
    {
        if (!userHasCollectionEditPermissions(request)) {
        return errorResponse("processBuildCollection", NO_PERMISSIONS_ERROR);
        }

        return runCommand(request, GS2PerlConstructor.BUILD);
    }

    protected Element processModifyMetadata(Element request)
    {

        // There are two types of operations whereby metadata gets modified:
        // - document including document-meta editing: user needs document editing powers
        // - adding user comments: user just needs an account and needs to be logged in
        // We handle both cases in this service.

        Element param_list = (Element) GSXML.getChildByTagName(request, GSXML.PARAM_ELEM + GSXML.LIST_MODIFIER);
        HashMap<String, Serializable> params = GSXML.extractParams(param_list, false);
        
        String metaserver_command = (String) params.get("a"); // e.g. set-archives-metadata or set-metadata-array
        boolean supportsSettingMultipleMeta = metaserver_command.equals("set-metadata-array") ? true : false;
        String json_str = (String) params.get("json"); // String or null if no param named "json"

        String[] docids = null;
        

        if (userHasCollectionEditPermissions(request, params)) { // means user can modify ANY metadata

        // if dealing with an array of meta, then parse out the docids from the json
        if(supportsSettingMultipleMeta) {
            docids = getDocIdsWithOptFilter(json_str, null);
        } // else set-meta operation on single metadata field of single doc, 
          // and docid will be obtained in runCommand() where it's needed

        } else {
        // check if user logged in
        // shouldn't be able to do any meta modification if not logged in

        UserContext context = new UserContext(request);
        if (context.getUsername().equals("")) {
            
            return errorResponse("processModifyMetadata", "Cannot modify any metadata when not logged in.");
        } else { // User is logged in at least, see whether they can do any restricted set-meta ops
            // that are open to regular users (those without permissions to edit this collection).
            // For now, there's only one restricted set-meta operation open to any logged in users
            // who don't otherwise have editing permissions for the collection: adding user comments.
            
            boolean isAddingUserComments = false;
            Pattern allowedMetaFieldsPattern = Pattern.compile("^(username|usertimestamp|usercomment)$");
            if(supportsSettingMultipleMeta) {
            
            docids = getDocIdsWithOptFilter(json_str, allowedMetaFieldsPattern);
            if(docids != null) {
                isAddingUserComments = true;
            }
            } else {
            String metaname = (String) params.get("metaname");
            if(isAllowedToSetMeta(metaname, allowedMetaFieldsPattern)) {
                isAddingUserComments = true;
            }
            }
        
            if(!isAddingUserComments) { // logged in user is attempting to set meta outside restricted set,
                 // In this case, they're attempting to set meta not related to user comments
            return errorResponse("processModifyMetadata", NO_PERMISSIONS_ERROR);
            }
        }
        }
        
        // wait until we can reserve the collection for processing
        waitUntilReady(request);
    
        
        // process
        Element response = runCommand(request, GS2PerlConstructor.MODIFY_METADATA_SERVER, docids);
        
        if (response.getElementsByTagName(GSXML.ERROR_ELEM).getLength() <= 0) // if no errors, wait for process to finish
        {
            Element statusElem = (Element) response.getElementsByTagName(GSXML.STATUS_ELEM).item(0);
            String id = statusElem.getAttribute("pid");
            
            GS2PerlListener currentListener = this.listeners.get(id);
            int statusCode = currentListener.getStatus();
            while (!GSStatus.isCompleted(statusCode))
            {
                // wait for the process, and keep checking the status code
                // there is probably a better way to do this.
                try
                {       
                    Thread.currentThread().sleep(100);
                }
                catch (Exception e)
                { // ignore
                }
                statusCode = currentListener.getStatus();
            }       
        }       
        
        Element statusElem = (Element) response.getElementsByTagName(GSXML.STATUS_ELEM).item(0);
        String statusString = GSXML.getNodeText(statusElem);
        statusString += " and monitored until done."; 
        // check for errors
        int status_code = Integer.parseInt(statusElem.getAttribute(GSXML.STATUS_ERROR_CODE_ATT));
        if (GSStatus.isError(status_code)) {
            logger.info("Got error status code: " + status_code);
            statusString += "But got error status code: " + status_code;
        } else { // check for Construction event errors
            String id = statusElem.getAttribute("pid");
            GS2PerlListener currentListener = this.listeners.get(id);
            status_code = currentListener.getStatus();
            if (GSStatus.isError(status_code))
            {
                logger.info("xxxx Got construction event error. Error status code: " + status_code);
                statusString += "But got construction event error, status code: " + status_code;
                // add the rest of the messages to the statusElem node
                statusString += "\n" + currentListener.getUpdate(); 
                statusElem.setAttribute(GSXML.STATUS_ERROR_CODE_ATT, Integer.toString(currentListener.getStatus()));
            }           
        }       
        // can finally set statusString
        GSXML.setNodeText(statusElem, statusString);
        
        // release hold on collection
        signalReady(request);
        return response;
        
    }

    protected Element processActivateCollection(Element request)
    {

        if (!userHasCollectionEditPermissions(request)) {
        return errorResponse("processActivateCollection", NO_PERMISSIONS_ERROR);
        }

        // this activates the collection on disk. but now we need to tell
        // the MR about it. but we have to wait until the process is finished.
        Element param_list = (Element) GSXML.getChildByTagName(request, GSXML.PARAM_ELEM + GSXML.LIST_MODIFIER);
        HashMap<String, Serializable> params = GSXML.extractParams(param_list, false);
        String coll_name = (String) params.get(COL_PARAM);
        String lang = request.getAttribute(GSXML.LANG_ATT);

        UserContext userContext = new UserContext(request);
        String request_type = request.getAttribute(GSXML.TYPE_ATT);
        
        // now we de-activate the collection before running activate.pl, and then re-activate at end 
        // So activate.pl only does the moving, no activation. This way will prevent java from launching 
        // perl, exiting and then leaving dangling file handles (on index/text/col.gdb) in perl.
        if (!request_type.equals(GSXML.REQUEST_TYPE_STATUS)) {          
            systemRequest("delete", coll_name, null, userContext); // deactivate collection
        }   

        Element response = runCommand(request, GS2PerlConstructor.ACTIVATE); // if request is for STATUS, then this won't run activate.pl

        Element status = (Element) GSXML.getChildByTagName(response, GSXML.STATUS_ELEM);

        // check for finished
        int status_code = Integer.parseInt(status.getAttribute(GSXML.STATUS_ERROR_CODE_ATT));
        if (GSStatus.isCompleted(status_code) && GSStatus.isError(status_code))
        {
            // we shouldn't carry out the next bit, just return the response
            return response;
        }
        String id = status.getAttribute(GSXML.STATUS_PROCESS_ID_ATT);
        GS2PerlListener listener = this.listeners.get(id);
        if (listener == null)
        {
            logger.error("somethings gone wrong, couldn't find the listener");
            status.setAttribute(GSXML.STATUS_ERROR_CODE_ATT, Integer.toString(GSStatus.ERROR));
            return response;
        }

        while (!GSStatus.isCompleted(status_code))
        {
            // wait for the process, and keep checking the status code
            // there is probably a better way to do this.
            try
            {
                Thread.currentThread().sleep(100);
            }
            catch (Exception e)
            { // ignore
            }
            status_code = listener.getStatus();
        }

        // add the rest of the messages to the status node
        Text t = status.getOwnerDocument().createTextNode("\n" + listener.getUpdate());
        status.appendChild(t);
        status.setAttribute(GSXML.STATUS_ERROR_CODE_ATT, Integer.toString(listener.getStatus()));
        if (GSStatus.isError(status_code))
        {
            return response; // without doing the next bit
        }

        t = status.getOwnerDocument().createTextNode("\n");
        status.appendChild(t);
        // once have got here, we assume
        // the first bit proceeded successfully, now reload the collection (sends a collection reactivation request)
        systemRequest("reload", coll_name, status, userContext); // this will append more messages to the status, and overwrite the error code att
        return response;

    }

    protected Element processDeleteCollection(Element request)
    {
        if (!userHasCollectionEditPermissions(request)) {
        return errorResponse("processDeleteCollection", NO_PERMISSIONS_ERROR);
        }

      Document result_doc = XMLConverter.newDOM();
        // the response to send back
        String name = GSPath.getFirstLink(request.getAttribute(GSXML.TO_ATT));
        Element response = result_doc.createElement(GSXML.RESPONSE_ELEM);
        response.setAttribute(GSXML.FROM_ATT, name);
        Element status = result_doc.createElement(GSXML.STATUS_ELEM);
        response.appendChild(status);
        Text t = null; // the text node for the error/success message
        String lang = request.getAttribute(GSXML.LANG_ATT);
        String request_type = request.getAttribute(GSXML.TYPE_ATT);

        Element param_list = (Element) GSXML.getChildByTagName(request, GSXML.PARAM_ELEM + GSXML.LIST_MODIFIER);
        HashMap<String, Serializable> params = GSXML.extractParams(param_list, false);

        boolean get_status_only = false;
        if (request_type.equals(GSXML.REQUEST_TYPE_STATUS))
        {
            get_status_only = true;
        }
        if (get_status_only)
        {
            // at the moment, delete is synchronous. but it may take ages so should do the command in another thread maybe? in which case we will want to ask for status
            logger.error("had a status request for delete - this shouldn't happen!!");
            //t = result_doc.createTextNode("");
            //status.appendChild(t);
            status.setAttribute(GSXML.STATUS_ERROR_CODE_ATT, Integer.toString(GSStatus.ERROR));
            return response;
        }
        String coll_name = (String) params.get(COL_PARAM);
        String[] args = { coll_name };
        File coll_dir = new File(GSFile.collectionBaseDir(this.site_home, coll_name));
        // check that the coll is there in the first place
        if (!coll_dir.exists())
        {
            t = result_doc.createTextNode(getTextString("delete.exists_error", lang, args));
            status.appendChild(t);
            status.setAttribute(GSXML.STATUS_ERROR_CODE_ATT, Integer.toString(GSStatus.ERROR));
            return response;
        }

        // try to delete the directory
        if (!GSFile.deleteFile(coll_dir))
        {
            t = result_doc.createTextNode(getTextString("delete.delete_error", lang, args));
            status.setAttribute(GSXML.STATUS_ERROR_CODE_ATT, Integer.toString(GSStatus.ERROR));
            status.appendChild(t);
            return response;
        }

        UserContext userContext = new UserContext(request);

        systemRequest("delete", coll_name, status, userContext);
        return response;
    }

    protected Element processReloadCollection(Element request)
    {
        if (!userHasCollectionEditPermissions(request)) {
        return errorResponse("processReloadCollection", NO_PERMISSIONS_ERROR);
        }

      Document result_doc = XMLConverter.newDOM();
        // the response to send back
        String name = GSPath.getFirstLink(request.getAttribute(GSXML.TO_ATT));
        Element response = result_doc.createElement(GSXML.RESPONSE_ELEM);
        response.setAttribute(GSXML.FROM_ATT, name);
        Element status = result_doc.createElement(GSXML.STATUS_ELEM);
        response.appendChild(status);
        Text t = null; // the text node for the error/success message

        String lang = request.getAttribute(GSXML.LANG_ATT);
        String request_type = request.getAttribute(GSXML.TYPE_ATT);

        Element param_list = (Element) GSXML.getChildByTagName(request, GSXML.PARAM_ELEM + GSXML.LIST_MODIFIER);
        HashMap<String, Serializable> params = GSXML.extractParams(param_list, false);

        boolean get_status_only = false;
        if (request_type.equals(GSXML.REQUEST_TYPE_STATUS))
        {
            get_status_only = true;
        }
        if (get_status_only)
        {
            // reload is synchronous - this makes no sense
            logger.error("had a status request for reload - this shouldn't happen!!");
            //t = result_doc.createTextNode("");
            //status.appendChild(t);
            status.setAttribute(GSXML.STATUS_ERROR_CODE_ATT, Integer.toString(GSStatus.ERROR));
            return response;
        }

        String coll_name = (String) params.get(COL_PARAM);

        UserContext userContext = new UserContext(request);

        systemRequest("reload", coll_name, status, userContext);
        return response;

    }

    /**
     * send a configure request to the message router action name should be
     * "delete" or "reload" response will be put into the status element
     */
    protected void systemRequest(String operation, String coll_name, Element status, UserContext userContext)
    {
        // send the request to the MR
      Document doc = XMLConverter.newDOM();
        Element message = doc.createElement(GSXML.MESSAGE_ELEM);
        Element request = GSXML.createBasicRequest(doc, GSXML.REQUEST_TYPE_SYSTEM, "", userContext);
        message.appendChild(request);
        Element command = doc.createElement(GSXML.SYSTEM_ELEM);
        request.appendChild(command);
        command.setAttribute(GSXML.SYSTEM_MODULE_TYPE_ATT, GSXML.COLLECTION_ELEM);
        command.setAttribute(GSXML.SYSTEM_MODULE_NAME_ATT, coll_name);

        if (operation.equals("delete"))
        {
            command.setAttribute(GSXML.TYPE_ATT, GSXML.SYSTEM_TYPE_DEACTIVATE);
        }
        else if (operation.equals("reload"))
        {
            command.setAttribute(GSXML.TYPE_ATT, GSXML.SYSTEM_TYPE_ACTIVATE);
        }
        else
        {
            logger.error("invalid action name passed to systemRequest:" + operation);
            return;
        }
        request.appendChild(command);
        Node response = this.router.process(message); // at the moment, get no info in response so ignore it
        Text t;
        String[] args = { coll_name };

        if (status != null)
        {
            if (response == null)
            {
              t = status.getOwnerDocument().createTextNode(getTextString(operation + ".configure_error", userContext.getLanguage(), args));
                status.setAttribute(GSXML.STATUS_ERROR_CODE_ATT, Integer.toString(GSStatus.ERROR));
                status.appendChild(t);
                return;
            }

            // if we got here, we have succeeded!
            t = status.getOwnerDocument().createTextNode(getTextString(operation + ".success", userContext.getLanguage(), args));
            status.setAttribute(GSXML.STATUS_ERROR_CODE_ATT, Integer.toString(GSStatus.SUCCESS));
            status.appendChild(t);
        }
    }

    /**
     * configure the service module for now, all services have type=build - need
     * to think about this
     */
    public boolean configure(Element info, Element extra_info)
    {
        if (!super.configure(info, extra_info))
        {
            return false;
        }

        logger.info("configuring GS2Construct");

        Element e = null;
        // hard code in the services for now

        // set up short_service_info_ - for now just has name and type

        e = this.desc_doc.createElement(GSXML.SERVICE_ELEM);
        e.setAttribute(GSXML.TYPE_ATT, GSXML.SERVICE_TYPE_PROCESS);
        e.setAttribute(GSXML.NAME_ATT, NEW_SERVICE);
        this.short_service_info.appendChild(e);

        e = this.desc_doc.createElement(GSXML.SERVICE_ELEM);
        e.setAttribute(GSXML.TYPE_ATT, GSXML.SERVICE_TYPE_PROCESS);
        e.setAttribute(GSXML.NAME_ATT, IMPORT_SERVICE);
        this.short_service_info.appendChild(e);

        e = this.desc_doc.createElement(GSXML.SERVICE_ELEM);
        e.setAttribute(GSXML.TYPE_ATT, GSXML.SERVICE_TYPE_PROCESS);
        e.setAttribute(GSXML.NAME_ATT, BUILD_SERVICE);
        this.short_service_info.appendChild(e);

        e = this.desc_doc.createElement(GSXML.SERVICE_ELEM);
        e.setAttribute(GSXML.TYPE_ATT, GSXML.SERVICE_TYPE_PROCESS);
        e.setAttribute(GSXML.NAME_ATT, ACTIVATE_SERVICE);
        this.short_service_info.appendChild(e);

        e = this.desc_doc.createElement(GSXML.SERVICE_ELEM);
        e.setAttribute(GSXML.TYPE_ATT, GSXML.SERVICE_TYPE_PROCESS);
        e.setAttribute(GSXML.NAME_ATT, BUILD_AND_ACTIVATE_SERVICE);
        this.short_service_info.appendChild(e);

        e = this.desc_doc.createElement(GSXML.SERVICE_ELEM);
        e.setAttribute(GSXML.TYPE_ATT, GSXML.SERVICE_TYPE_PROCESS);
        e.setAttribute(GSXML.NAME_ATT, DELETE_SERVICE);
        this.short_service_info.appendChild(e);

        e = this.desc_doc.createElement(GSXML.SERVICE_ELEM);
        e.setAttribute(GSXML.TYPE_ATT, GSXML.SERVICE_TYPE_PROCESS);
        e.setAttribute(GSXML.NAME_ATT, RELOAD_SERVICE);
        this.short_service_info.appendChild(e);

        //e = this.desc_doc.createElement(GSXML.SERVICE_ELEM);
        //e.setAttribute(GSXML.TYPE_ATT, GSXML.SERVICE_TYPE_PROCESS);
        //e.setAttribute(GSXML.NAME_ATT, ADD_DOC_SERVICE);
        //this.short_service_info.appendChild(e);

        e = this.desc_doc.createElement(GSXML.SERVICE_ELEM);
        e.setAttribute(GSXML.TYPE_ATT, GSXML.SERVICE_TYPE_PROCESS);
        e.setAttribute(GSXML.NAME_ATT, MODIFY_METADATA_SERVICE);
        this.short_service_info.appendChild(e);

        return true;
    }

    protected Element runCommand(Element request, int type) {
        return runCommand(request, type, null);
    }

    /** returns a response element */
    protected Element runCommand(Element request, int type, String[] docids)
    {
        Document result_doc = XMLConverter.newDOM();
        // the response to send back
        String name = GSPath.getFirstLink(request.getAttribute(GSXML.TO_ATT));
        Element response = result_doc.createElement(GSXML.RESPONSE_ELEM);
        response.setAttribute(GSXML.FROM_ATT, name);
        Element status = result_doc.createElement(GSXML.STATUS_ELEM);
        response.appendChild(status);

        String lang = request.getAttribute(GSXML.LANG_ATT);
        String request_type = request.getAttribute(GSXML.TYPE_ATT);

        Element param_list = (Element) GSXML.getChildByTagName(request, GSXML.PARAM_ELEM + GSXML.LIST_MODIFIER);
        
        //GSXML.elementToLogAsString("###      Extracted param_list: ", param_list, true);
        //GSXML.elementToLogAsUnicodeDebugString("### DEBUG Extracted param_list: ", param_list, true);
        
        HashMap<String, Serializable> params = GSXML.extractParams(param_list, false);

        boolean get_status_only = false;
        if (request_type.equals(GSXML.REQUEST_TYPE_STATUS))
        {
            get_status_only = true;
        }

        // just check for status messages if that's all that's required
        if (get_status_only)
        {
            String id = (String) params.get(PROCESS_ID_PARAM);
            status.setAttribute(GSXML.STATUS_PROCESS_ID_ATT, id);
            GS2PerlListener listener = this.listeners.get(id);
            if (listener == null)
            {
                Text t = result_doc.createTextNode(getTextString("general.process_id_error", lang));
                status.appendChild(t);
                status.setAttribute(GSXML.STATUS_ERROR_CODE_ATT, Integer.toString(GSStatus.ERROR));
            }
            else
            {
                Text t = result_doc.createTextNode(listener.getUpdate());
                status.appendChild(t);
                status.setAttribute(GSXML.STATUS_ERROR_CODE_ATT, Integer.toString(listener.getStatus()));
                // check that we actually should be removing the listener here
                if (listener.isFinished())
                { // remove this listener - its job is done
                    this.listeners.remove(id); // not working
                }
            }
            return response;

        }

        // do the actual command
        String coll_name = null;
        if (type == GS2PerlConstructor.NEW)
        {
            String coll_title = (String) params.get(NEW_COL_TITLE_PARAM);
            coll_name = createNewCollName(coll_title);
        }
        else
        {
            coll_name = (String) params.get(COL_PARAM);
        }

        // makes a paramList of the relevant params
        Element other_params = extractOtherParams(params, type);

        //create the constructor to do the work
        GS2PerlConstructor constructor = new GS2PerlConstructor("perl_build");
        if (!constructor.configure())
        {
            Text t = result_doc.createTextNode(getTextString("general.configure_constructor_error", lang));
            status.appendChild(t);
            status.setAttribute(GSXML.STATUS_ERROR_CODE_ATT, Integer.toString(GSStatus.ERROR));
            return response;
        }

        constructor.setSiteHome(this.site_home);
        constructor.setLibraryName(this.library_name);
        constructor.setCollectionName(coll_name);
        constructor.setActionType(type);
        constructor.setProcessParams(other_params);
        if (type == GS2PerlConstructor.IMPORT)
        {
            constructor.setManifestFile(this.site_home + File.separator + "collect" + File.separator + params.get(COL_PARAM) + File.separator + "manifests" + File.separator + "tempManifest.xml");
        }
        else if (type == GS2PerlConstructor.MODIFY_METADATA_SERVER) {
            StringBuffer querystring = new StringBuffer();
            
            // convert params into a single string again?
            Set<Map.Entry<String, Serializable>> entries = params.entrySet();
            Iterator<Map.Entry<String, Serializable>> i = entries.iterator();
            
            String oid = null;

            while (i.hasNext()) {

                Map.Entry<String, Serializable> entry = i.next();
                String paramname = entry.getKey();
                paramname = paramname.replace("s1.", ""); // replaces all occurrences
                if (paramname.equals("collection")) {
                    paramname = "c";
                }
                if (paramname.equals("d")){
                    oid = (String) entry.getValue();
                }
                
                String paramvalue = (String) entry.getValue();

                // This will be used to set QUERY_STRING in the environment, see build/GS2PerlConstructor.java
                // Need to also ensure that special characters in param values won't get clobbered on Windows by perl/CGI.pm,
                // see also https://www.nntp.perl.org/group/perl.perl5.porters/2016/10/msg240120.html
                // Therefore URL encode CGI param values in the query_string, as at https://stackoverflow.com/questions/10786042/java-url-encoding-of-query-string-parameters
        
                // perl/CGI.pm doesn't like us URL encoding the entire QUERY_STRING such as the equal sign between each paramName and paramValue.
                // So we URL encode each paramValue separately, which is done in GS2Construct.java::runCommand()
                querystring.append(paramname + "=" + urlEncodeValue(paramname, paramvalue));
                if (i.hasNext()) {
                    querystring.append("&");
                }
            }
            
            if(oid != null) { // if we have only one oid
            markDocumentInFlatDatabase("R", coll_name, OID.getTop(oid));
            } else if (docids != null) { // check if we are dealing with many doc ids, as cold in theory happen when set-metadata-array is called
            
            for(int index = 0; index < docids.length; index++) {
                String docid = docids[index];
                markDocumentInFlatDatabase("R", coll_name, OID.getTop(docid));
            }
            } else {
            String msg = getTextString("general.no_valid_docid_error", lang);
            logger.error("*** " + msg);
            Text t = result_doc.createTextNode(msg);
            status.appendChild(t);
            status.setAttribute(GSXML.STATUS_ERROR_CODE_ATT, Integer.toString(GSStatus.ERROR));
            return response;
            }
            
            constructor.setQueryString(querystring.toString());
        }

        GS2PerlListener listener = new GS2PerlListener();
        constructor.addListener(listener);
        constructor.start();

        String id = newID();
        this.listeners.put(id, listener);

        status.setAttribute(GSXML.STATUS_PROCESS_ID_ATT, id);
        status.setAttribute(GSXML.STATUS_ERROR_CODE_ATT, Integer.toString(GSStatus.ACCEPTED));
        Text t = result_doc.createTextNode(getTextString("general.process_start", lang));
        status.appendChild(t);
        return response;
    }

    //************************
    // some helper functions
    //************************

    private String urlEncodeValue(String paramName, String paramVal) {
        String oldParamVal = paramVal;
        try{
            paramVal = URLEncoder.encode(paramVal, "UTF-8");            
            // Better way as per https://stackoverflow.com/questions/10786042/java-url-encoding-of-query-string-parameters
            // but our release kits' Java is too old for importing java.nio.charset.StandardCharsets
            //paramVal = URLEncoder.encode(paramVal, StandardCharsets.UTF_8.name());            
        } catch(UnsupportedEncodingException uee) {
            logger.warn("**** Unable to encode query_string param " + paramName + " in UTF-8, so attempting to continue with its unencoded value."); // don't output param value to log, in case of sensitive data?
            paramVal = oldParamVal; 
        }
        return paramVal;
    }
    
    /** parse the collect directory and return a list of collection names */
    protected String[] getCollectionList()
    {

        File collectDir = new File(GSFile.collectDir(this.site_home));
        if (!collectDir.exists())
        {
            logger.error("couldn't find collect dir: " + collectDir.toString());
            return null;
        }
        logger.info("GS2Construct: reading thru directory " + collectDir.getPath() + " to find collections.");
        File[] contents = collectDir.listFiles();
        int num_colls = 0;
        for (int i = 0; i < contents.length; i++)
        {
            if (contents[i].isDirectory() && !contents[i].getName().startsWith("CVS"))
            {
                num_colls++;
            }
        }

        String[] names = new String[num_colls];

        for (int i = 0, j = 0; i < contents.length; i++)
        {
            if (contents[i].isDirectory())
            {
                String colName = contents[i].getName();
                if (!colName.startsWith("CVS"))
                {
                    names[j] = colName;
                    j++;
                }

            }
        }

        return names;

    }

    /** ids used for process id */
    private int current_id = 0;

    private String newID()
    {
        current_id++;
        return Integer.toString(current_id);
    }

    /** creates a new short name from the collection title */
    protected String createNewCollName(String coll_title)
    {

        String base_name = null;
        // take the first 6 letters
        if (coll_title.length() < 6)
        {
            base_name = coll_title;
        }
        else
        {
            base_name = coll_title.substring(0, 6);
        }
        File coll_dir = new File(GSFile.collectionBaseDir(this.site_home, base_name));
        if (!coll_dir.exists())
        { // this name is ok - not used yet
            return base_name;
        }

        // now we have to make a new name until we get a good one
        // try name1, name2 name3 etc
        int i = 0;
        while (coll_dir.exists())
        {
            i++;
            coll_dir = new File(GSFile.collectionBaseDir(this.site_home, base_name + Integer.toString(i)));
        }
        return base_name + Integer.toString(i);

    }

    /**
     * takes the params from the request (in the HashMap) and extracts any that
     * need to be passed to the constructor and puts them into a paramList
     * element
     */
    protected Element extractOtherParams(HashMap<String, Serializable> params, int type)
    {
      Document doc = XMLConverter.newDOM();
        Element param_list = doc.createElement(GSXML.PARAM_ELEM + GSXML.LIST_MODIFIER);
        if (type == GS2PerlConstructor.NEW)
        {
            Element param = doc.createElement(GSXML.PARAM_ELEM);
            param.setAttribute(GSXML.NAME_ATT, "creator");
            param.setAttribute(GSXML.VALUE_ATT, (String) params.get(CREATOR_PARAM));

            param_list.appendChild(param);
            param = doc.createElement(GSXML.PARAM_ELEM);
            param.setAttribute(GSXML.NAME_ATT, "about");
            param.setAttribute(GSXML.VALUE_ATT, (String) params.get(NEW_COL_ABOUT_PARAM));
            param_list.appendChild(param);
            param = doc.createElement(GSXML.PARAM_ELEM);
            param.setAttribute(GSXML.NAME_ATT, "title");
            param.setAttribute(GSXML.VALUE_ATT, (String) params.get(NEW_COL_TITLE_PARAM));
            param_list.appendChild(param);
            param = doc.createElement(GSXML.PARAM_ELEM);
            param.setAttribute(GSXML.NAME_ATT, "buildtype");
            param.setAttribute(GSXML.VALUE_ATT, (String) params.get(BUILDTYPE_PARAM));
            param_list.appendChild(param);
            return param_list;
        }

        // other ones dont have params yet
        return null;
    }

    protected void waitUntilReady(Element request)
    {
        Element param_list = (Element) GSXML.getChildByTagName(request, GSXML.PARAM_ELEM + GSXML.LIST_MODIFIER);
        HashMap<String, Serializable> params = GSXML.extractParams(param_list, false);

        String collection = (String) params.get(COL_PARAM);

        if (checkCollectionIsNotBusy(collection))
        {
            return;
        }

        while (!checkCollectionIsNotBusy(collection)) // When the collection ceases to be busy, we place a hold on it
        {
            try
            {
                Thread.currentThread().sleep(1000);
            }
            catch (Exception ex)
            {
                ex.printStackTrace();
            }
        }
    }

    protected void signalReady(Element request)
    {
        Element param_list = (Element) GSXML.getChildByTagName(request, GSXML.PARAM_ELEM + GSXML.LIST_MODIFIER);
        HashMap<String, Serializable> params = GSXML.extractParams(param_list, false);

        String collection = (String) params.get(COL_PARAM);

        collectionOperationMap.remove(collection);
    }

    // If collection is NOT busy, then reserve it
    protected synchronized boolean checkCollectionIsNotBusy(String collection)
    {
        if (collectionOperationMap.get(collection) == null)
        {
            collectionOperationMap.put(collection, true);
            return true;
        }
        return false;
    }

    protected boolean isAllowedToSetMeta(String metaname, Pattern allowedMetaFieldsPattern) 
    {
    if(allowedMetaFieldsPattern == null) { // null when user has edit permissions, so they can set any meta
        ///logger.info("### User has permissions to set any meta.");
        return true;
    }
    if(metaname == null) {
        ///logger.info("### Can't check null metaname against pattern");
        return false;
    }
    
    Matcher m = allowedMetaFieldsPattern.matcher(metaname);
    if(!m.matches()) {
        ///logger.info("### metaname: " + metaname + " doesn't match allowed allowed fields: " + allowedMetaFieldsPattern.toString());
        return false;
    } else {
        return true;
    }
    }
    
    protected String[] getDocIdsWithOptFilter(String json_str, Pattern filterFields) // boolean strictOrPermissible
    {
    if(json_str == null) {
        logger.error("### Shouldn't be happening: null json string");
        return null;
    }

    String[] docids = null;

    // check that the name of each metadata being set matches the pattern filterFields.
    // The presence of any other meta means something other than adding user comments is being attempted,
    // which is invalid
    try {
        
        JSONArray docInfoList = new JSONArray(json_str);
        docids = new String[docInfoList.length()];
        for(int index = 0; index < docInfoList.length(); index++) {
        JSONObject docInfo = docInfoList.getJSONObject(index);
        if(docInfo.has("metatable")) { // should exist for metadata arrays
            
            docids[index] = docInfo.getString("docid"); // should exist if metatable existed

            ///logger.info("@@@ Found docid: " + docids[index]);

            JSONArray metatable = docInfo.getJSONArray("metatable");
            for(int i = 0; i < metatable.length(); i++) {
            JSONObject meta = metatable.getJSONObject(i);

            String metaname = meta.getString("metaname");
            ///logger.info("### metaname: " + metaname);
            
            if(!isAllowedToSetMeta(metaname, filterFields)) {
                return null;
            }
            }
        }
        }
    } catch(JSONException jsonex) {
        logger.error("Exception when parsing json string: " + json_str);
        logger.error(jsonex);
        
    }
    
    // if we're here, then it means that the JSON only asked for username|usercomment|usertimestamp meta
    // meaning that the setmeta operation was a valid user comment operation.
    // In that case, we have a docid for which we need to add a user comment 
    // set-metadata-array can take more docids, but doesn't happen for a user comment. And one comment
    // is added at a time, but 3 meta fields are set for each comment: username, usercomment and timestamp
    // hence the use of set-meta-array.
    return docids;

    }

    protected Element errorResponse(String serviceName, String errorMsg) {
    Document result_doc = XMLConverter.newDOM();
    Element result = GSXML.createBasicResponse(result_doc, serviceName);
    GSXML.addError(result, errorMsg);
    return result;
    }

    /** Copy from DebugService.userHasEditPermissions
     This function checks that the user is logged in and that the user 
     is in the right group to edit the collection */
    protected boolean userHasCollectionEditPermissions(Element request) {
    Element param_list = (Element) GSXML.getChildByTagName(request, GSXML.PARAM_ELEM + GSXML.LIST_MODIFIER);
    HashMap<String, Serializable> params = GSXML.extractParams(param_list, false);

    return userHasCollectionEditPermissions(request, params);

    }

    protected boolean userHasCollectionEditPermissions(Element request, HashMap<String, Serializable> params) {
    String collection = (String) params.get(COL_PARAM); // could be null on newcoll operation


    UserContext context = new UserContext(request);
    if(collection == null) {
    return !context.getUsername().equals("");
    }

    /* 
    // FOR DEBUGGING
    Set<Map.Entry<String, Serializable>> entries = params.entrySet();
    Iterator<Map.Entry<String, Serializable>> i = entries.iterator();
    
    StringBuffer parametersLine = new StringBuffer();
    while (i.hasNext()) {
    
    Map.Entry<String, Serializable> entry = i.next();
    String paramname = entry.getKey();
    String paramvalue = (String) entry.getValue();
    
    parametersLine.append("\t" + paramname + ": " + paramvalue + "\n");
    }
    
    logger.info("XXXXXXXXXXXXX PARAMETERS:\n" + parametersLine);
    */

    for (String group : context.getGroups()) {
      // administrator always has permission
      if (group.equals("administrator")) {
    return true;
      }
      // all-collections-editor can edit any collection
      if (!collection.equals("")) {
    if (group.equals("all-collections-editor")) {
      return true;
    }
    if (group.equals(collection+"-collection-editor")) {
      return true;
    }
      }
    }
    // haven't found a group with edit permissions
    return false;
    
  }
    protected void markDocumentInFlatDatabase(String mark, String collection, String oid) {
        
        Document msg_doc = XMLConverter.newDOM();
        Element message = msg_doc.createElement(GSXML.MESSAGE_ELEM);
        UserContext userContext = new UserContext();
        Element query_request = GSXML.createBasicRequest(msg_doc, GSXML.REQUEST_TYPE_DESCRIBE , collection, userContext);       
        message.appendChild(query_request);
        Element result = (Element) this.router.process(message);
        Element resp_elem = (Element) GSXML.getChildByTagName(result, GSXML.RESPONSE_ELEM);
        Element coll_elem = (Element) GSXML.getChildByTagName(resp_elem, GSXML.COLLECTION_ELEM);
        String dbtype = coll_elem.getAttribute(GSXML.DB_TYPE_ATT);
        
        SimpleCollectionDatabase coll_db = new SimpleCollectionDatabase(dbtype);
        if (!coll_db.databaseOK())
        {
            logger.error("Couldn't create the collection database of type " + dbtype);
            return;
        }
        
        // Open database for reading. It may not exist if collection is pre-built without archives (such as demo collections)
        String coll_db_file = GSFile.archivesDatabaseFile(this.site_home, collection, dbtype);
        if (!coll_db.openDatabase(coll_db_file, SimpleCollectionDatabase.READ))
        {
            logger.error("Could not open collection archives database. Database doesn't exist or else somebody's already using it?");
            return;
        }
        // now we know we have an archives folder
        String old_value = coll_db.getValue(oid);
        String new_value = "<index-status>" + mark;
        if(old_value == null) {
            logger.error("### null old_value in flat DB for oid " + oid);
        } else {
            new_value = old_value.replace("<index-status>B", "<index-status>" + mark);
            logger.info("### Replacing db entry for oid " + oid + " which has old_value " + old_value);
            logger.info("### with new value " + new_value);
                    
        }
        // Close database for reading
        coll_db.closeDatabase();

        if (!coll_db.openDatabase(coll_db_file, SimpleCollectionDatabase.WRITE))
            {
            logger.error("Could not open collection archives database. Somebody already using this database!");
            return;
            }
        
        coll_db.setValue(oid, new_value);
        
        coll_db.closeDatabase();        
    }
}