[openemr.git] / controllers / C_Document.class.php

<?php
// 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.

require_once(dirname(__FILE__) . "/../library/classes/Controller.class.php");
require_once(dirname(__FILE__) . "/../library/classes/Document.class.php");
require_once(dirname(__FILE__) . "/../library/classes/CategoryTree.class.php");
require_once(dirname(__FILE__) . "/../library/classes/TreeMenu.php");
require_once(dirname(__FILE__) . "/../library/classes/Note.class.php");
require_once(dirname(__FILE__) . "/../library/classes/CouchDB.class.php");

class C_Document extends Controller {

        var $template_mod;
        var $documents;
        var $document_categories;
        var $tree;
        var $_config;
        var $file_path;
        

        function C_Document($template_mod = "general") {
                parent::Controller();
                $this->documents = array();
                $this->template_mod = $template_mod;
                $this->assign("FORM_ACTION", $GLOBALS['webroot']."/controller.php?" . $_SERVER['QUERY_STRING']);
                $this->assign("CURRENT_ACTION", $GLOBALS['webroot']."/controller.php?" . "document&");
                
                //get global config options for this namespace
                $this->_config = $GLOBALS['oer_config']['documents'];
                if($GLOBALS['document_storage_method']==1){
                        $this->file_path = $GLOBALS['OE_SITE_DIR'].'/documents/temp/';
                }
                else{
                $this->file_path = $this->_config['repository'] . preg_replace("/[^A-Za-z0-9]/","_",$_GET['patient_id']) . "/";
                }
                $this->_args = array("patient_id" => $_GET['patient_id']);
                
                $this->assign("STYLE", $GLOBALS['style']);
                $t = new CategoryTree(1);
                //print_r($t->tree);
                $this->tree = $t;
        }
        
        function upload_action($patient_id,$category_id) {
                $category_name = $this->tree->get_node_name($category_id);
                $this->assign("category_id", $category_id);
                $this->assign("category_name", $category_name);
                $this->assign("hide_encryption", $GLOBALS['hide_document_encryption'] );
                $this->assign("patient_id", $patient_id);
                $activity = $this->fetch($GLOBALS['template_dir'] . "documents/" . $this->template_mod . "_upload.html");
                $this->assign("activity", $activity);
                return $this->list_action($patient_id);
        }
        
        function upload_action_process() {
                $couchDB = false;
                $harddisk = false;
                if($GLOBALS['document_storage_method']==0){
                        $harddisk = true;
                }
                if($GLOBALS['document_storage_method']==1){
                        $couchDB = true;
                }
                                
                if ($_POST['process'] != "true")
                        return;
                        
                $doDecryption = false;
                $encrypted = $_POST['encrypted'];
                $passphrase = $_POST['passphrase'];
                if ( !$GLOBALS['hide_document_encryption'] && 
                    $encrypted && $passphrase ) {
                    $doDecryption = true;
                }
                        
                if (is_numeric($_POST['category_id'])) {        
                        $category_id = $_POST['category_id'];
                }
                if (is_numeric($_POST['patient_id'])) {
                        $patient_id = $_POST['patient_id'];
                }
                        
                foreach ($_FILES as $file) {
                  $fname = $file['name'];
                  $err = "";
                  if ($file['error'] > 0 || empty($file['name']) || $file['size'] == 0) {
                        $fname = $file['name'];
                        if (empty($fname)) {
                                $fname = htmlentities("<empty>");
                        }
                        $error = "Error number: " . $file['error'] . " occured while uploading file named: " . $fname . "\n";
                        if ($file['size'] == 0) {
                                $error .= "The system does not permit uploading files of with size 0.\n";
                        }
                        
                  }
                  else {
                        
                        if (!file_exists($this->file_path)) {
                                if (!mkdir($this->file_path,0700)) {
                                        $error .= "The system was unable to create the directory for this upload, '" . $this->file_path . "'.\n";
                                }
                        }
                    if ( $_POST['destination'] != '' ) {
                        $fname = $_POST['destination'];
                    }
                        $fname = preg_replace("/[^a-zA-Z0-9_.]/","_",$fname);
                        if (file_exists($this->file_path.$fname)) {
                                $error .= xl('File with same name already exists at location:','','',' ') . $this->file_path . "\n";
                                $fname = basename($this->_rename_file($this->file_path.$fname));
                                $file['name'] = $fname;
                                $error .= xl('Current file name was changed to','','',' ') . $fname ."\n";
                        }
                        
                        if ( $doDecryption ) {
                                $tmpfile = fopen( $file['tmp_name'], "r" );
                                $filetext = fread( $tmpfile, $file['size'] );
                                $plaintext = $this->decrypt( $filetext, $passphrase );
                                fclose($tmpfile);
                                unlink( $file['tmp_name'] );
                                $tmpfile = fopen( $file['tmp_name'], "w+" );
                                fwrite( $tmpfile, $plaintext );
                                fclose( $tmpfile );
                                $file['size'] = filesize( $file['tmp_name'] );
                        }
                        $docid = '';
                        $resp = '';                     
                        if($couchDB == true){
                                $couch = new CouchDB();
                                $docname = $_SESSION['authId'].$patient_id.$encounter.$fname.date("%Y-%m-%d H:i:s");
                                $docid = $couch->stringToId($docname);
                                $tmpfile = fopen( $file['tmp_name'], "rb" );
                                $filetext = fread( $tmpfile, $file['size'] );                           
                                fclose( $tmpfile );
                                //--------Temporarily writing the file for calculating the hash--------//
                                //-----------Will be removed after calculating the hash value----------//
                                $temp_file = fopen($this->file_path.$fname,"w");
                                fwrite($temp_file,$filetext);
                                fclose($temp_file);
                                //---------------------------------------------------------------------//
                                
                                $json = json_encode(base64_encode($filetext));
                                $db = $GLOBALS['couchdb_dbase'];
                                $data = array($db,$docid,$patient_id,$encounter,$file['type'],$json);
                                $resp = $couch->check_saveDOC($data);
                                if(!$resp->id || !$resp->_rev){
                                        $data = array($db,$docid,$patient_id,$encounter);
                                        $resp = $couch->retrieve_doc($data);
                                        $docid = $resp->_id;
                                        $revid = $resp->_rev;
                                }
                                else{
                                        $docid = $resp->id;
                                        $revid = $resp->rev;
                                }
                                if(!$docid && !$revid){ //if couchdb save failed
                                        $error .=  "<font color='red'><b>".xl("The file could not be saved to CouchDB.") . "</b></font>\n";
                                        if($GLOBALS['couchdb_log']==1){
                                                ob_start();
                                                var_dump($resp);
                                                $couchError=ob_get_clean();
                                                $log_content = date('Y-m-d H:i:s')." ==> Uploading document: ".$fname."\r\n";
                                                $log_content .= date('Y-m-d H:i:s')." ==> Failed to Store document content to CouchDB.\r\n";
                                                $log_content .= date('Y-m-d H:i:s')." ==> Document ID: ".$docid."\r\n";
                                                $log_content .= date('Y-m-d H:i:s')." ==> ".print_r($data,1)."\r\n";
                                                $log_content .= $couchError;
                                                $this->document_upload_download_log($patient_id,$log_content);//log error if any, for testing phase only
                                        }
                                }                               
                        }
                        if($harddisk == true){
                                $uploadSuccess = false;
                                if(move_uploaded_file($file['tmp_name'],$this->file_path.$fname)){
                                        $uploadSuccess = true;
                                }
                                else{
                                        $error .= xl("The file could not be succesfully stored, this error is usually related to permissions problems on the storage system")."\n";
                                        }
                        }
                        $this->assign("upload_success", "true");
                        $d = new Document();
                        $d->storagemethod = $GLOBALS['document_storage_method'];
                        if($harddisk == true)
                                $d->url = "file://" .$this->file_path.$fname;
                        else
                                $d->url = $fname;
                        if($couchDB == true){
                                $d->couch_docid = $docid;
                                $d->couch_revid = $revid;
                        }
                        if ($file['type'] == 'text/xml') {
                                $d->mimetype = 'application/xml';
                        }
                        else {
                                $d->mimetype = $file['type'];
                        }                                 
                        $d->size = $file['size'];
                        $d->owner = $_SESSION['authUserID'];                    
                        $sha1Hash = sha1_file( $this->file_path.$fname );
                        if($couchDB == true){
                                //Removing the temporary file which is used to create the hash
                                unlink($this->file_path.$fname);
                        }
                        $d->hash = $sha1Hash;
                        $d->type = $d->type_array['file_url'];
                        $d->set_foreign_id($patient_id);
                        if($harddisk == true || ($couchDB == true && $docid && $revid)){
                                $d->persist();
                                $d->populate();
                        }
                        $this->assign("file",$d);
                        
                        if (is_numeric($d->get_id()) && is_numeric($category_id)){
                                $sql = "REPLACE INTO categories_to_documents set category_id = '" . $category_id . "', document_id = '" . $d->get_id() . "'";
                                $d->_db->Execute($sql);
                        }
                        if($GLOBALS['couchdb_log']==1 && $log_content!=''){
                                $log_content .= "\r\n\r\n";
                                $this->document_upload_download_log($patient_id,$log_content);
                        }
                }
                }
                $this->assign("error", nl2br($error));
                //$this->_state = false;
                $_POST['process'] = "";
                //return $this->fetch($GLOBALS['template_dir'] . "documents/" . $this->template_mod . "_upload.html");
        }
        
        function note_action_process($patient_id) {
                
                if ($_POST['process'] != "true")
                        return;
                        
                $n = new Note();
                parent::populate_object($n);
                $n->persist();
                
                $this->_state = false;
                $_POST['process'] = "";
                return $this->view_action($patient_id,$n->get_foreign_id());            
        }

        function default_action() {
                return $this->list_action();
        }
        
        function view_action($patient_id="",$doc_id) {
                // Added by Rod to support document delete:
                global $gacl_object, $phpgacl_location;
                global $ISSUE_TYPES;

                require_once(dirname(__FILE__) . "/../library/acl.inc");
                require_once(dirname(__FILE__) . "/../library/lists.inc");

                $d = new Document($doc_id);     
                $n = new Note();
                
                $notes = $n->notes_factory($doc_id);
                
                $this->assign("file", $d);
                $this->assign("web_path", $this->_link("retrieve") . "document_id=" . $d->get_id() . "&");
                $this->assign("NOTE_ACTION",$this->_link("note"));
                $this->assign("MOVE_ACTION",$this->_link("move") . "document_id=" . $d->get_id() . "&process=true");
                $this->assign("hide_encryption", $GLOBALS['hide_document_encryption'] );

                // Added by Rod to support document delete:
                $delete_string = '';
                if (acl_check('admin', 'super')) {
                        $delete_string = "<a href='' class='css_button' onclick='return deleteme(" . $d->get_id() .
                                ")'><span><font color='red'>" . xl('Delete') . "</font></span></a>";
                }
                $this->assign("delete_string", $delete_string);
                $this->assign("REFRESH_ACTION",$this->_link("list"));
                
                $this->assign("VALIDATE_ACTION",$this->_link("validate") .
                        "document_id=" . $d->get_id() . "&process=true");

                // Added by Rod to support document date update:
                $this->assign("DOCDATE", $d->get_docdate());
                $this->assign("UPDATE_ACTION",$this->_link("update") .
                        "document_id=" . $d->get_id() . "&process=true");

                // Added by Rod to support document issue update:
                $issues_options = "<option value='0'>-- " . xl('Select Issue') . " --</option>";
                $ires = sqlStatement("SELECT id, type, title, begdate FROM lists WHERE " .
                        "pid = $patient_id " . // AND enddate IS NULL " .
                        "ORDER BY type, begdate");
                while ($irow = sqlFetchArray($ires)) {
                        $desc = $irow['type'];
                        if ($ISSUE_TYPES[$desc]) $desc = $ISSUE_TYPES[$desc][2];
                        $desc .= ": " . $irow['begdate'] . " " . htmlspecialchars(substr($irow['title'], 0, 40));
                        $sel = ($irow['id'] == $d->get_list_id()) ? ' selected' : '';
                        $issues_options .= "<option value='" . $irow['id'] . "'$sel>$desc</option>";
                }
                $this->assign("ISSUES_LIST", $issues_options);

                $this->assign("notes",$notes);
                
                $this->_last_node = null;
                
                $menu  = new HTML_TreeMenu();
                
                //pass an empty array because we don't want the documents for each category showing up in this list box
                $rnode = $this->_array_recurse($this->tree->tree,array());
                $menu->addItem($rnode);
                $treeMenu_listbox  = &new HTML_TreeMenu_Listbox($menu, array("promoText" => xl('Move Document to Category:')));
                
                $this->assign("tree_html_listbox",$treeMenu_listbox->toHTML());
                
                $activity = $this->fetch($GLOBALS['template_dir'] . "documents/" . $this->template_mod . "_view.html");
                $this->assign("activity", $activity);
                
                return $this->list_action($patient_id);
        }
        
        function encrypt( $plaintext, $key, $cypher = 'tripledes', $mode = 'cfb' )
    {
        $td = mcrypt_module_open( $cypher, '', $mode, '');
        $iv = mcrypt_create_iv( mcrypt_enc_get_iv_size( $td ), MCRYPT_RAND );
        mcrypt_generic_init( $td, $key, $iv );
        $crypttext = mcrypt_generic( $td, $plaintext );
        mcrypt_generic_deinit( $td );
        return $iv.$crypttext;
    }

    function decrypt( $crypttext, $key, $cypher = 'tripledes', $mode = 'cfb' )
    {
        $plaintext = '';
        $td = mcrypt_module_open( $cypher, '', $mode, '' );
        $ivsize = mcrypt_enc_get_iv_size( $td) ;
        $iv = substr( $crypttext, 0, $ivsize );
        $crypttext = substr( $crypttext, $ivsize );
        if( $iv )
        {
            mcrypt_generic_init( $td, $key, $iv );
            $plaintext = mdecrypt_generic( $td, $crypttext );
        }
        return $plaintext;
    }
        
        
        function retrieve_action($patient_id="",$document_id,$as_file=true,$original_file=true) {
            
            $encrypted = $_POST['encrypted'];
                $passphrase = $_POST['passphrase'];
                $doEncryption = false;
                if ( !$GLOBALS['hide_document_encryption'] &&
                    $encrypted == "true" && 
                    $passphrase ) {
                    $doEncryption = true;        
                }
                
                //controller function ruins booleans, so need to manually re-convert to booleans
                if ($as_file == "true") {
                        $as_file=true;
                }
                else if ($as_file == "false") {
                        $as_file=false;    
                }
                if ($original_file == "true") {
                        $original_file=true;
                }
                else if ($original_file == "false") {
                        $original_file=false;   
                }
            
                $d = new Document($document_id);
                $url =  $d->get_url();
                $storagemethod = $d->get_storagemethod();
                $couch_docid = $d->get_couch_docid();
                $couch_revid = $d->get_couch_revid();
                
                if($couch_docid && $couch_revid && $original_file){
                        $couch = new CouchDB();
                        $data = array($GLOBALS['couchdb_dbase'],$couch_docid);
                        $resp = $couch->retrieve_doc($data);
                        $content = $resp->data;
                        if($content=='' && $GLOBALS['couchdb_log']==1){                         
                                $log_content = date('Y-m-d H:i:s')." ==> Retrieving document\r\n";
                                $log_content = date('Y-m-d H:i:s')." ==> URL: ".$url."\r\n";
                                $log_content .= date('Y-m-d H:i:s')." ==> CouchDB Document Id: ".$couch_docid."\r\n";
                                $log_content .= date('Y-m-d H:i:s')." ==> CouchDB Revision Id: ".$couch_revid."\r\n";
                                $log_content .= date('Y-m-d H:i:s')." ==> Failed to fetch document content from CouchDB.\r\n";
                                $log_content .= date('Y-m-d H:i:s')." ==> Will try to download file from HardDisk if exists.\r\n\r\n";
                                $this->document_upload_download_log($d->get_foreign_id(),$log_content);
                                die(xl("File retrieval from CouchDB failed"));
                        }
                        header('Content-Description: File Transfer');
                        header('Content-Transfer-Encoding: binary');
                        header('Expires: 0');
                        header('Cache-Control: must-revalidate, post-check=0, pre-check=0');
                        header('Pragma: public');
                        $tmpcouchpath = $GLOBALS['OE_SITE_DIR'].'/documents/temp/couch_'.date("YmdHis").$d->get_url_file();
                        $fh = fopen($tmpcouchpath,"w");
                        fwrite($fh,base64_decode($content));
                        fclose($fh);
                        $f = fopen($tmpcouchpath,"r");
                        if ( $doEncryption ) {
                                $filetext = fread( $f, filesize($tmpcouchpath) );
                                $ciphertext = $this->encrypt( $filetext, $passphrase );
                                $tmpfilepath = $GLOBALS['temporary_files_dir'];
                                $tmpfilename = "/encrypted_".$d->get_url_file();
                                $tmpfile = fopen( $tmpfilepath.$tmpfilename, "w+" );
                                fwrite( $tmpfile, $ciphertext );
                                fclose( $tmpfile );
                                header('Content-Disposition: attachment; filename='.$tmpfilename );
                                header("Content-Type: application/octet-stream" );
                                header("Content-Length: " . filesize( $tmpfilepath.$tmpfilename ) );
                                ob_clean();
                                flush();
                                readfile( $tmpfilepath.$tmpfilename );
                                unlink( $tmpfilepath.$tmpfilename );
                        } else {
                                header("Content-Disposition: " . ($as_file ? "attachment" : "inline") . "; filename=\"" . basename($d->get_url()) . "\"");
                                header("Content-Type: " . $d->get_mimetype());
                                header("Content-Length: " . filesize($tmpcouchpath));
                                fpassthru($f);
                        }
                        fclose($f);
                        if($content!='')
                        unlink($tmpcouchpath);
                        exit;//exits only if file download from CouchDB is successfull. 
                }
                //strip url of protocol handler
                $url = preg_replace("|^(.*)://|","",$url);
                
                //change full path to current webroot.  this is for documents that may have
                //been moved from a different filesystem and the full path in the database
                //is not current.  this is also for documents that may of been moved to
                //different patients
                // NOTE that $from_filename and basename($url) are the same thing
                $from_all = explode("/",$url);
                $from_filename = array_pop($from_all);
                $from_patientid = array_pop($from_all);
    if($couch_docid && $couch_revid){
        //for couchDB no URL is available in the table, hence using the foreign_id which is patientID
        $temp_url = $GLOBALS['OE_SITE_DIR'] . '/documents/temp/' . $d->get_foreign_id() . '_' . $from_filename;
        
        }
        else{
        $temp_url = $GLOBALS['OE_SITE_DIR'] . '/documents/' . $from_patientid . '/' . $from_filename;
        }
        
                if (file_exists($temp_url)) {
                        $url = $temp_url;
                }
                 
                 
                if (!file_exists($url)) {
                        echo xl('The requested document is not present at the expected location on the filesystem or there are not sufficient permissions to access it.','','',' ') . $url;
                
                }
                else {
                        if ($original_file) {
                            //normal case when serving the file referenced in database
                header('Content-Description: File Transfer');
                header('Content-Transfer-Encoding: binary');
                header('Expires: 0');
                header('Cache-Control: must-revalidate, post-check=0, pre-check=0');
                header('Pragma: public');
                            $f = fopen($url,"r");
                            if ( $doEncryption ) {
                                        $filetext = fread( $f, filesize($url) );
                                $ciphertext = $this->encrypt( $filetext, $passphrase );
                                $tmpfilepath = $GLOBALS['temporary_files_dir'];
                                $tmpfilename = "/encrypted_".$d->get_url_file();
                                $tmpfile = fopen( $tmpfilepath.$tmpfilename, "w+" );
                    fwrite( $tmpfile, $ciphertext );
                    fclose( $tmpfile );
                    header('Content-Disposition: attachment; filename='.$tmpfilename );
                                header("Content-Type: application/octet-stream" );
                                header("Content-Length: " . filesize( $tmpfilepath.$tmpfilename ) );
                                ob_clean();
                            flush();
                            readfile( $tmpfilepath.$tmpfilename );
                    unlink( $tmpfilepath.$tmpfilename );
                            } else {
                                header("Content-Disposition: " . ($as_file ? "attachment" : "inline") . "; filename=\"" . basename($d->get_url()) . "\"");
                                header("Content-Type: " . $d->get_mimetype());
                                header("Content-Length: " . filesize($url));
                                fpassthru($f);
                            }
                            exit;
                        }
                        else {
                            //special case when retrieving a document that has been converted to a jpg and not directly referenced in database
                                $convertedFile = substr(basename($url), 0, strrpos(basename($url), '.')) . '_converted.jpg';                        
                                if($couch_docid && $couch_revid){
                                $url = $GLOBALS['OE_SITE_DIR'] . '/documents/temp/' . $convertedFile;
                                }
                                else{
                                $url = $GLOBALS['OE_SITE_DIR'] . '/documents/' . $from_patientid . '/' . $convertedFile;
                }
                                header("Pragma: public");
                            header("Expires: 0");
                            header("Cache-Control: must-revalidate, post-check=0, pre-check=0");
                            header("Content-Disposition: " . ($as_file ? "attachment" : "inline") . "; filename=\"" . basename($url) . "\"");
                            header("Content-Type: image/jpeg");
                            header("Content-Length: " . filesize($url));
                            $f = fopen($url,"r");
                            fpassthru($f);
                                if($couch_docid && $couch_revid){
                                fclose($f);
                                unlink($url);
                                $url=str_replace("_converted.jpg",'.pdf',$url);
                                unlink($url);
                                }
                            exit;
                        }
                }               
        }
        
        function queue_action($patient_id="") {
                $messages = $this->_tpl_vars['messages'];
                $queue_files = array();
                
                //see if the repository exists and it is a directory else error
                if (file_exists($this->_config['repository']) && is_dir($this->_config['repository'])) {
                        $dir = opendir($this->_config['repository']);
                        //read each entry in the directory
                        while (($file = readdir($dir)) !== false) {
                                //concat the filename and path
                                $file = $this->_config['repository'] .$file;
                                $file_info = array();
                                //if the filename is a file get its info and put into a tmp array
                                if (is_file($file) && strpos(basename($file),".") !== 0) {
                                        $file_info['filename'] = basename($file);
                                        $file_info['mtime'] = date("m/d/Y H:i:s",filemtime($file));
                                        $d = Document::document_factory_url("file://" . $file);
                                        preg_match("/^([0-9]+)_/",basename($file),$patient_match);
                                        $file_info['patient_id'] = $patient_match[1];
                                        $file_info['document_id'] = $d->get_id();
                                        $file_info['web_path'] = $this->_link("retrieve",true) . "document_id=" . $d->get_id() . "&";
                                        
                                        //merge the tmp array into the larger array
                                        $queue_files[] = $file_info; 
                                }
                }
                closedir($dir);
                }
                else {
                        $messages .= "The repository directory does not exist, it is not a directory or there are not sufficient permissions to access it. '" . $this->config['repository'] . "'\n";    
                }
                
                
                $this->assign("queue_files",$queue_files);
                $this->_last_node = null;
                
                $menu  = new HTML_TreeMenu();
                
                //pass an empty array because we don't want the documents for each category showing up in this list box
                $rnode = $this->_array_recurse($this->tree->tree,array());
                $menu->addItem($rnode);
                $treeMenu_listbox  = &new HTML_TreeMenu_Listbox($menu, array());
                
                $this->assign("tree_html_listbox",$treeMenu_listbox->toHTML());
                
                $this->assign("messages",nl2br($messages));
                return $this->fetch($GLOBALS['template_dir'] . "documents/" . $this->template_mod . "_queue.html");
        }
        
        function queue_action_process() {       
                if ($_POST['process'] != "true")
                        return;
                
                $messages = $this->_tpl_vars['messages'];       
                
                //build a category tree so we can have a list of category ids that are valid
                $ct = new CategoryTree(1);
                $categories = $ct->_id_name;
                
                //see if there were and posted files and assign them
                $files = null;
                is_array($_POST['files']) ? $files = $_POST['files']: $files = array();         
                
                //loop through posted files
                foreach($files as $doc_id=> $file) {
                        //only operate on files checked as active
                        if (!$file['active']) continue;
                        
                        //run basic validation checks 
                        if (!is_numeric($file['patient_id']) || !is_numeric($file['category_id']) || !is_numeric($doc_id)) {
                                $messages .= "Error processing file '" . $file['name'] ."' the patient id must be a number and the category must exist.\n";
                                continue;       
                        }
                        
                        //validate that the pod exists
                        $d = new Document($doc_id);
                        $sql = "SELECT pid from patient_data where pubpid = '" . $file['patient_id'] . "'";
                        $result = $d->_db->Execute($sql);
                        
                        if (!$result || $result->EOF) {
                                //patient id does not exist
                                $messages .= "Error processing file '" . $file['name'] ." the specified patient id '" . $file['patient_id'] . "' could not be found.\n";
                                continue;
                        }
                        
                        //validate that the category id exists
                        if (!isset($categories[$file['category_id']])) {
                                $messages .= "Error processing file '" . $file['name'] . " the specified category with id '" . $file['category_id'] . "' could not be found.\n";
                                continue;
                        }
                        
                        //now do the work of moving the file
                        $new_path = $this->_config['repository'] . $file['patient_id'] ."/";
                        
                        //see if the patient dir exists in the repository and create if not
                        if (!file_exists($new_path)) {                          
                                if (!mkdir($new_path,0700)) {
                                        $messages .= "The system was unable to create the directory for this upload, '" . $this->file_path . "'.\n";
                                        continue;
                                }
                        }
                        
                        //fname is the name of the file after it is moved
                        $fname = $file['name'];
                        
                        //see if patient autonumbering is used in this filename, if so strip out the autonumber part
                        preg_match("/^([0-9]+)_/",basename($fname),$patient_match);
                        if ($patient_match[1] == $file['patient_id']) {
                                $fname = preg_replace("/^([0-9]+)_/","",$fname);
                        }
                        
                        //filenames should not have funny chars
                        $fname = preg_replace("/[^a-zA-Z0-9_.]/","_",$fname);
                        
                        //see if there is an existing file with the same name and rename as necessary
                        if (file_exists($new_path.$file['name'])) {
                                $messages .= "File with same name already exists at location: " . $new_path . "\n";
                                $fname = basename($this->_rename_file($new_path.$file['name']));
                                $messages .= "Current file name was changed to " . $fname ."\n";        
                        }
                        
                        //now move the file
                        if (rename($this->_config['repository'].$file['name'],$new_path.$fname)) {
                                $messages .= "File " . $fname . " moved to patient id '" . $file['patient_id'] ."' and category '" . $categories[$file['category_id']]['name'] . "' successfully.\n";
                                $d->url = "file://" .$new_path.$fname;
                                $d->set_foreign_id($file['patient_id']);
                                $d->set_mimetype($mimetype);
                                $d->persist();
                                $d->populate();
                                
                                if (is_numeric($d->get_id()) && is_numeric($file['category_id'])) {
                                  $sql = "REPLACE INTO categories_to_documents set category_id = '" . $file['category_id'] . "', document_id = '" . $d->get_id() . "'";
                                  $d->_db->Execute($sql);
                                }
                        }
                        else {
                                $error .= "The file could not be succesfully stored, this error is usually related to permissions problems on the storage system.\n";
                        }
                }
                        $this->assign("messages",$messages);
                        $_POST['process'] = "";
        }
        
        function move_action_process($patient_id="",$document_id) {
                if ($_POST['process'] != "true")
                        return;
                
                $new_category_id = $_POST['new_category_id'];
                $new_patient_id = $_POST['new_patient_id'];
                
                //move to new category
                if (is_numeric($new_category_id) && is_numeric($document_id)) {
                        $sql = "UPDATE categories_to_documents set category_id = '" . $new_category_id . "' where document_id = '" . $document_id ."'";
                        $messages .= xl('Document moved to new category','','',' \'') . $this->tree->_id_name[$new_category_id]['name']  . xl('successfully.','','\' ') . "\n";
                        //echo $sql;
                        $this->tree->_db->Execute($sql);
                }
                
                //move to new patient
                if (is_numeric($new_patient_id) && is_numeric($document_id)) {
                        $d = new Document($document_id);
                        // $sql = "SELECT pid from patient_data where pubpid = '" . $new_patient_id . "'";
                        $sql = "SELECT pid from patient_data where pid = '" . $new_patient_id . "'";
                        $result = $d->_db->Execute($sql);
                        
                        if (!$result || $result->EOF) {
                                //patient id does not exist
                                $messages .= xl('Document could not be moved to patient id','','',' \'') . $new_patient_id  . xl('because that id does not exist.','','\' ') . "\n";
                        }
                        else {
                        
                                $couch_docid = $d->get_couch_docid();
                                $couch_revid = $d->get_couch_revid();
                                //set the new patient in CouchDB
                                $couchsavefailed=false;
                                if($couch_docid && $couch_revid){
                                $couch = new CouchDB();
                                $db = $GLOBALS['couchdb_dbase'];
                                $data=array($db,$couch_docid);
                                $couchresp=$couch->retrieve_doc($data);
                                //CouchDB doesnot support updating a single value in a document.
                                //Have to retrieve the entire document,update the necessary value and save again
                                list($db,$docid,$revid,$patient_id,$encounter,$type,$json) = $data;
                                $data=array($db,$couch_docid,$couch_revid,$new_patient_id,$couchresp->encounter,$couchresp->mimetype,json_encode($couchresp->data));
                                $resp = $couch->update_doc($data);
                                //Sometimes the response from CouchDB is not available
                                //still it would have saved in the DB. Hence check one more time
                                if(!$resp->_id || !$resp->_rev){
                                        $data = array($db,$couch_docid,$new_patient_id,$couchresp->encounter);
                                        $resp = $couch->retrieve_doc($data);
                                        
                                        
                                }
                                if($resp->_rev ==$couch_revid){
                                        $couchsavefailed=true;
                                        }
                                else{
                                $d->set_couch_revid($resp->_rev);
                                }
                                }
                                
                                
                                //set the new patient in mysql
                                $d->set_foreign_id($new_patient_id);
                                $d->persist();
                                $this->_state = false;
                                if(!$couchsavefailed){
                                
                                $messages .= xl('Document moved to patient id','','',' \'') . $new_patient_id  . xl('successfully.','','\' ') . "\n";
                                }
                                else{
                                
                                $messages .= xl('Document moved to patient id','','',' \'') . $new_patient_id  . xl('Failed.','','\' ') . "\n";
                                }
                                $this->assign("messages",$messages);
                                return $this->list_action($patient_id);
                        }
                }
                //in this case return the document to the queue instead of moving it
                elseif (strtolower($new_patient_id) == "q" && is_numeric($document_id)) {
                        $d = new Document($document_id);
                        $new_path = $this->_config['repository'];
                        $fname = $d->get_url_file();

                        //see if there is an existing file with the same name and rename as necessary
                        if (file_exists($new_path.$d->get_url_file())) {
                                $messages .= "File with same name already exists in the queue.\n";
                                $fname = basename($this->_rename_file($new_path.$d->get_url_file()));
                                $messages .= "Current file name was changed to " . $fname ."\n";        
                        }
                         
                        //now move the file
                        if (rename($d->get_url_filepath(),$new_path.$fname)) {
                                $d->url = "file://" .$new_path.$fname;
                                $d->set_foreign_id("");
                                $d->persist();
                                $d->persist();
                                $d->populate();
                                
                                $sql = "DELETE FROM categories_to_documents where document_id =" . $d->_db->qstr($document_id);
                                $d->_db->Execute($sql);
                                $messages .= "Document returned to queue successfully.\n";
                                
                        }
                        else {
                                $messages .= "The file could not be succesfully stored, this error is usually related to permissions problems on the storage system.\n";
                        }

                        $this->_state = false;
                        $this->assign("messages",$messages);
                        return $this->list_action($patient_id);
                }
                
                $this->_state = false;
                $this->assign("messages",$messages);
                return $this->view_action($patient_id,$document_id);
        }
        
        function validate_action_process($patient_id="", $document_id) {

                $d = new Document($document_id);
                if($d->couch_docid && $d->couch_revid){
                        $file_path = $GLOBALS['OE_SITE_DIR'].'/documents/temp/';
                        $url = $file_path.$d->get_url();
                        $couch = new CouchDB();
                        $data = array($GLOBALS['couchdb_dbase'],$d->couch_docid);
                        $resp = $couch->retrieve_doc($data);
                        $content = $resp->data;
                        //--------Temporarily writing the file for calculating the hash--------//
                        //-----------Will be removed after calculating the hash value----------//
                        $temp_file = fopen($url,"w");
                        fwrite($temp_file,base64_decode($content));
                        fclose($temp_file);                     
                }
                else{
                $url =  $d->get_url();

                //strip url of protocol handler
                $url = preg_replace("|^(.*)://|","",$url);

                //change full path to current webroot.  this is for documents that may have
                //been moved from a different filesystem and the full path in the database
                //is not current.  this is also for documents that may of been moved to
                //different patients
                // NOTE that $from_filename and basename($url) are the same thing
                $from_all = explode("/",$url);
                $from_filename = array_pop($from_all);
                $from_patientid = array_pop($from_all);
                $temp_url = $GLOBALS['OE_SITE_DIR'] . '/documents/' . $from_patientid . '/' . $from_filename;
                if (file_exists($temp_url)) {
                        $url = $temp_url;
                }

            if ($_POST['process'] != "true") {
                        die("process is '" . $_POST['process'] . "', expected 'true'");
                        return;
                }
                }
                $d = new Document( $document_id );
                $current_hash = sha1_file( $url );
                $messages = xl('Current Hash').": ".$current_hash."<br>";
                $messages .= xl('Stored Hash').": ".$d->get_hash()."<br>";
                if ( $d->get_hash() == '' ) {
                    $d->hash = $current_hash;
                    $d->persist();
                    $d->populate();
                    $messages .= xl('Hash did not exist for this file. A new hash was generated.');
                } else if ( $current_hash != $d->get_hash() ) {
                    $messages .= xl('Hash does not match. Data integrity has been compromised.');
                } else {
                    $messages .= xl('Document passed integrity check.');
                }
                $this->_state = false;
                $this->assign("messages", $messages);
                if($d->couch_docid && $d->couch_revid){
                        //Removing the temporary file which is used to create the hash
                        unlink($GLOBALS['OE_SITE_DIR'].'/documents/temp/'.$d->get_url());
                }
                return $this->view_action($patient_id, $document_id);
        }

        // Added by Rod for metadata update.
        //
        function update_action_process($patient_id="", $document_id) {
                
                if ($_POST['process'] != "true") {
                        die("process is '" . $_POST['process'] . "', expected 'true'");
                        return;
                }

                $docdate = $_POST['docdate'];
                $docname = $_POST['docname'];
                $issue_id = $_POST['issue_id'];

                if (is_numeric($document_id)) {
                    $messages = '';
                    $d = new Document( $document_id );
                    $file_name = $d->get_url_file();
                    if ( $docname != '' &&
                         $docname != $file_name ) {
                        $path = $d->get_url_filepath();
                        $path = str_replace( $file_name, "", $path );  
                        $new_url = $this->_rename_file( $path.$docname );
                    if ( rename( $d->get_url(), $new_url ) ) {
                        // check the "converted" file, and delete it if it exists. It will be regenerated when report is run
                        $url = preg_replace("|^(.*)://|","",$d->get_url());
                        $convertedFile = substr(basename($url), 0, strrpos(basename($url), '.')) . '_converted.jpg';                        
                    $url = $GLOBALS['OE_SITE_DIR'] . '/documents/' . $patient_id . '/' . $convertedFile;
                                if ( file_exists( $url ) ) {
                                    unlink( $url );
                                }
                                $d->url = $new_url;
                    $d->persist();
                    $d->populate();
                                $messages .= xl('Document successfully renamed.')."<br>";
                        } else {
                                $messages .= xl('The file could not be succesfully renamed, this error is usually related to permissions problems on the storage system.')."<br>";
                        }
                    }
                 
                        if (preg_match('/^\d\d\d\d-\d+-\d+$/', $docdate)) {
                                $docdate = "'$docdate'";
                        } else {
                                $docdate = "NULL";
                        }
                        if (!is_numeric($issue_id)) {
                                $issue_id = 0;
                        }
                        $couch_docid = $d->get_couch_docid();
                        $couch_revid = $d->get_couch_revid();
                        if($couch_docid && $couch_revid ){
                        $sql = "UPDATE documents SET docdate = $docdate, url = '".$_POST['docname']."', " .
                                        "list_id = '$issue_id' " .
                                        "WHERE id = '$document_id'";
                        $this->tree->_db->Execute($sql);
                        
                        }
                        else{
                        $sql = "UPDATE documents SET docdate = $docdate, " .
                                "list_id = '$issue_id' " .
                                "WHERE id = '$document_id'";
                        $this->tree->_db->Execute($sql);        
                        }
                        $messages .= xl('Document date and issue updated successfully') . "<br>";
                }

                $this->_state = false;
                $this->assign("messages", $messages);
                return $this->view_action($patient_id, $document_id);
        }

        function list_action($patient_id = "") {
                $this->_last_node = null;
                $categories_list = $this->tree->_get_categories_array($patient_id);
                //print_r($categories_list);
                                
                $menu  = new HTML_TreeMenu();
                $rnode = $this->_array_recurse($this->tree->tree,$categories_list);
                $menu->addItem($rnode);
                $treeMenu = &new HTML_TreeMenu_DHTML($menu, array('images' => 'images', 'defaultClass' => 'treeMenuDefault'));
                $treeMenu_listbox  = &new HTML_TreeMenu_Listbox($menu, array('linkTarget' => '_self'));
                
                $this->assign("tree_html",$treeMenu->toHTML());
                
                return $this->fetch($GLOBALS['template_dir'] . "documents/" . $this->template_mod . "_list.html");
        }
        
        /*
        *       This is a recursive function to rename a file to something that doesn't already exist.
        *       Modified in version 3.2.0 to place a counter within the filename (previously was placed at end)
        *        to ensure documents opened correctly by external browser viewers. If the counter is at the
        *        end of the file, then will use it (to continue to work with older files), however all new
        *        counters will be placed within filenames. 
        */
        function _rename_file($fname) {
                $file = basename($fname);
                $fparts = split("\.",$fname);
                $path = dirname($fname);
                if (count($fparts) > 1) {
                  if (is_numeric($fparts[count($fparts) -2]) && (count($fparts) > 2)) {
                        //increment the counter in filename
                        $fparts[count($fparts) -2] = $fparts[count($fparts) -2] + 1;
                        $fname = join(".",$fparts);
                  }
                  elseif (is_numeric($fparts[count($fparts) -1]) && $fparts[count($fparts) -1] < 1000) {
                        //increment counter at end of filename (so compatible with previous openemr version files
                        $fparts[count($fparts) -1] = $fparts[count($fparts) -1] + 1;
                        $fname = join(".",$fparts);
                  }
                  elseif (is_numeric($fparts[count($fparts) -1])) {
                        //leave date at end and place counter in filename
                        array_splice($fparts, -1, 0, "1");
                        $fname = join(".",$fparts);
                  }                 
                  else {
                        //add the counter to filename
                        array_splice($fparts, -1, 0, "1");
                        $fname = join(".",$fparts);
                  }
                }
                else { // (count($fparts) == 1)
                  //place counter at end of filename
                  array_push($fparts,"1");
                  $fname = join(".",$fparts);
                }
            
                if (file_exists($fname)) {
                        return $this->_rename_file($fname);
                }
                else {
                        return($fname); 
                }
        }
        
        function &_array_recurse($array,$categories = array()) {
                if (!is_array($array)) {
                        $array = array();       
                }
                $node = &$this->_last_node;
                $current_node = &$node;
                $expandedIcon = 'folder-expanded.gif';
                foreach($array as $id => $ar) {
                        $icon = 'folder.gif';
                        if (is_array($ar)  || !empty($id)) {
                          if ($node == null) {
                                //echo "r:" . $this->tree->get_node_name($id) . "<br>";
                            $rnode = new HTML_TreeNode(array("id" => $id, 'text' => $this->tree->get_node_name($id), 'link' => $this->_link("upload") . "parent_id=" . $id . "&", 'icon' => $icon, 'expandedIcon' => $expandedIcon, 'expanded' => false));
                            $this->_last_node = &$rnode;
                                $node = &$rnode;
                                $current_node =&$rnode;
                          }
                          else {
                                //echo "p:" . $this->tree->get_node_name($id) . "<br>";
                            $this->_last_node = &$node->addItem(new HTML_TreeNode(array("id" => $id, 'text' => $this->tree->get_node_name($id), 'link' => $this->_link("upload") . "parent_id=" . $id . "&", 'icon' => $icon, 'expandedIcon' => $expandedIcon)));
                            $current_node =&$this->_last_node;
                          }
                          
                          $this->_array_recurse($ar,$categories);
                        }
                        else {
                                if ($id === 0 && !empty($ar)) {
                                  $info = $this->tree->get_node_info($id);
                                  //echo "b:" . $this->tree->get_node_name($id) . "<br>";
                                  $current_node = &$node->addItem(new HTML_TreeNode(array("id" => $id, 'text' => $info['value'], 'link' => $this->_link("upload") . "parent_id=" . $id . "&", 'icon' => $icon, 'expandedIcon' => $expandedIcon)));
                                }
                                else {
                                        //there is a third case that is implicit here when title === 0 and $ar is empty, in that case we do not want to do anything
                                        //this conditional tree could be more efficient but working with recursive trees makes my head hurt, TODO
                                        if ($id !== 0 && is_object($node)) {
                                          //echo "n:" . $this->tree->get_node_name($id) . "<br>";
                                          $current_node = &$node->addItem(new HTML_TreeNode(array("id" => $id, 'text' => $this->tree->get_node_name($id), 'link' => $this->_link("upload") . "parent_id=" . $id . "&", 'icon' => $icon, 'expandedIcon' => $expandedIcon)));
                                          
                                        }
                                }
                        }       

                        // If there are documents in this document category, then add their
                        // attributes to the current node.
                        $icon = "file3.png";
                        if (is_array($categories[$id])) {
                                foreach ($categories[$id] as $doc) {
          if($this->tree->get_node_name($id) == "CCR"){
            $current_node->addItem(new HTML_TreeNode(array(
              'text' => $doc['docdate'] . ' ' . basename($doc['url']),
              'link' => $this->_link("view") . "doc_id=" . $doc['document_id'] . "&",
              'icon' => $icon,
              'expandedIcon' => $expandedIcon,
              'events' => array('Onclick' => "javascript:newwindow=window.open('ccr/display.php?type=CCR&doc_id=" . $doc['document_id'] . "','CCR');")
            )));
          }elseif($this->tree->get_node_name($id) == "CCD"){
            $current_node->addItem(new HTML_TreeNode(array(
              'text' => $doc['docdate'] . ' ' . basename($doc['url']),
              'link' => $this->_link("view") . "doc_id=" . $doc['document_id'] . "&",
              'icon' => $icon,
              'expandedIcon' => $expandedIcon,
              'events' => array('Onclick' => "javascript:newwindow=window.open('ccr/display.php?type=CCD&doc_id=" . $doc['document_id'] . "','CCD');")
            )));
          }else{
            $current_node->addItem(new HTML_TreeNode(array(
              'text' => $doc['docdate'] . ' ' . basename($doc['url']),
              'link' => $this->_link("view") . "doc_id=" . $doc['document_id'] . "&",
              'icon' => $icon,
              'expandedIcon' => $expandedIcon
            )));
          }
                                }
                        }

                }
                return $node;
        }
        
        //function for logging  the errors in writing file to CouchDB/Hard Disk
        function document_upload_download_log($patientid,$content){
                $log_path = $GLOBALS['OE_SITE_DIR']."/documents/couchdb/";
                $log_file = 'log.txt';
                if(!is_dir($log_path))
                    mkdir($log_path,0777,true);
                $LOG = fopen($log_path.$log_file,'a');
                fwrite($LOG,$content);
                fclose($LOG);
        }

}
//place to hold optional code
//$first_node = array_keys($t->tree);
                //$first_node = $first_node[0];
                //$node1 = new HTML_TreeNode(array('text' => $t->get_node_name($first_node), 'link' => "test.php", 'icon' => $icon, 'expandedIcon' => $expandedIcon, 'expanded' => true), array('onclick' => "alert('foo'); return false", 'onexpand' => "alert('Expanded')"));
                
                //$this->_last_node = &$node1;

?>