aces · samirdas · Apr 26, 2012 · Feb 7, 2012 · Feb 14, 2012 · Mar 1, 2012
diff --git a/SQL/0000-00-00-schema.sql b/SQL/0000-00-00-schema.sql
@@ -1097,6 +1097,28 @@ LOCK TABLES `query_gui_stored_queries` WRITE;
 /*!40000 ALTER TABLE `query_gui_stored_queries` ENABLE KEYS */;
 UNLOCK TABLES;
 
+--
+-- Table structure for table `query_gui_user_files`
+--
+DROP TABLE IF EXISTS `query_gui_user_files`;
+CREATE TABLE query_gui_user_files (
+    UserFileID integer auto_increment primary key,
+    UserID integer REFERENCES users(ID),
+    filename varchar(255),
+    downloadDate timestamp DEFAULT CURRENT_TIMESTAMP,
+    md5sum varchar(32),
+    status enum('ready', 'packaging', 'expired')
+);
+
+--
+-- Dumping data for table `query_gui_user_files`
+--
+
+LOCK TABLES `query_gui_user_files` WRITE;
+/*!40000 ALTER TABLE `query_gui_user_files` DISABLE KEYS */;
+/*!40000 ALTER TABLE `query_gui_user_files` ENABLE KEYS */;
+UNLOCK TABLES;
+
 --
 -- Table structure for table `session`
 --

diff --git a/SQL/2012-02-14-Query_GUI_Download.sql b/SQL/2012-02-14-Query_GUI_Download.sql
@@ -0,0 +1,8 @@
+CREATE TABLE query_gui_user_files (
+    UserFileID integer auto_increment primary key,
+    UserID integer REFERENCES users(ID),
+    filename varchar(255),
+    downloadDate timestamp DEFAULT CURRENT_TIMESTAMP,
+    md5sum varchar(32),
+    status enum('ready', 'packaging', 'expired')
+);
diff --git a/htdocs/downloads b/htdocs/downloads
@@ -0,0 +1 @@
+../userdownloads/
diff --git a/htdocs/dqgui_step3.js b/htdocs/dqgui_step3.js
@@ -1,5 +1,12 @@
 
-function executeQuery(){
+function executeQuery(sendTo){
+    if(sendTo == 'download') {
+        var oCbrainField=IFrameDoc.getElementById("download");
+        oCbrainField.value="execute";
+        var m = document.getElementById("message");
+        m.innerHTML = "Packaging your files. They'll be ready to download <a href=\"main.php?test_name=download_files\">here</a> in a few minutes."; 
+    }
+
     var oQueryField=IFrameDoc.getElementById("queryData");
     var oModeField=IFrameDoc.getElementById("mode");
     oModeField.value="executeQuery";
@@ -65,4 +72,4 @@ function querySaved(){
 
 function doNothing(){
     return true;  
-}
+}
diff --git a/htdocs/mri/jiv/get_file.php b/htdocs/mri/jiv/get_file.php
@@ -29,10 +29,28 @@
 if ($blessPass) {
     $imagePath  = $config->getSetting('imagePath');
     $imageFile = $imagePath."/".$_GET['file'];
-    if(!file_exists($imageFile)) exit;
-    $pf = fopen($imageFile, 'r');
-    fpassthru($pf);
-    fclose($pf);
+    if(file_exists($imageFile)) {
+        $pf = fopen($imageFile, 'r');
+        fpassthru($pf);
+        fclose($pf);
+    }
+} else {
+    // If the file isn't blessed because it's the wrong type or starts with a /,
+    // it's still available if it's under DownloadPath. We just check to make sure it doesn't
+    // have ".." in it  so that the user can't escape DownloadPath.
+    $downloadPath = $config->getSetting('DownloadPath');
+    $downloadFile = $downloadPath.$_GET['file'];
+    if(file_exists($downloadFile) && strrpos($_GET['file'], '..') === FALSE) {
+        header("Content-type: application/x-minc");
+        header("Content-Disposition: attachment; filename=\"".basename($_GET['file'])."\"");
+
+        $pf = fopen($downloadFile, 'r');
+        fpassthru($pf);
+        fclose($pf);
+        exit;
+    } else {
+        print "File not found\n";
+    }
 }
 
 function blessPassThrough($toBless) {
@@ -42,7 +60,7 @@ function blessPassThrough($toBless) {
         return false;    
     }
 
-    if (strrpos($toBless, '.jpg') || strrpos($toBless, '.raw_byte.gz') || strrpos($toBless, '.header')) {
+    if (strrpos($toBless, '.jpg') || strrpos($toBless, '.raw_byte.gz') || strrpos($toBless, '.header') || strrpos($toBless, '.mnc')) {
         return true;
     } 
 

diff --git a/htdocs/query_gui.php b/htdocs/query_gui.php
@@ -164,7 +164,18 @@
                         </select>
 </td></tr>
 <tr>
-<td><input type='button' value='Click here for your results' onclick='executeQuery()'></td></tr>
+<td>
+<input type='button' value='Click here for your results' onclick='executeQuery()'>
+<?
+$user = User::singleton();
+if($user->hasPermission('download_files')) {
+?>
+<input type='button' value='Click here to download files' onclick="executeQuery('download')"><span id="message">&nbsp;</span>
+<?
+}
+?>
+</td>
+</tr>
 </table>
 <p>
 <div id='thang'></div>

diff --git a/htdocs/query_gui_data_download.php b/htdocs/query_gui_data_download.php
@@ -24,13 +24,15 @@
 $config =& NDB_Config::singleton();
 $css = $config->getSetting('css');
 $studyTitle = $config->getSetting('title');
+$downloadPath= $config->getSetting('DownloadPath');
+print "Download Path: $downloadPath";
 
 $query = "";
 
 if(!empty($_GET['queryID'])) {
-
     // get the query
     $query = $DB->selectOne("SELECT query FROM query_gui_downloadable_queries WHERE queryID='$_GET[queryID]'");
+    $format = $_GET['format'];
 
     // run the query
     $results = array();
@@ -40,11 +42,29 @@
         exit;
     }
 	// add the description as the second row
-	foreach(array_keys($results[0]) AS $key) {
-	   $desc[$key] = $DB->selectOne("SELECT Description FROM parameter_type WHERE Name='$key'");
+    $files_cols = array();
+	foreach(array_keys($results[0]) AS $i => $key) {
+        $parameter_type = $DB->pselectRow("SELECT Description, IsFile FROM parameter_type WHERE Name=:key", array('key' => $key));
+	    $desc[$key] = $parameter_type['Description'];
+        if($parameter_type['IsFile']) {
+            $files_cols[] = $key;
+        }
 	}
 
 	$newResults[0] = $desc;
+    $files = array();
+	for($row=0; $row < count($results); $row++) {
+        foreach($files_cols as $col) {
+            if(!empty($results[$row][$col]) && ($format=='html' || $format=='download_files')) {
+                $file = $results[$row][$col];
+                if($format == 'html') {
+                    $results[$row][$col] = "<a href=\"mri/jiv/get_file.php?file=$file\">$file</a>";
+                } else if($format == 'download_files') {
+                    $files[] = $file;
+                }
+            }
+        }
+    }
 	for($i=0; $i < count($results); $i++) {
 	   $newResults[$i+1] = $results[$i];
 	}
@@ -62,7 +82,13 @@
     }
 
     // build the file buffer
-    list($buffer, $format) = buildFileBuffer($results, $_GET['format'], $css, $studyTitle);
+
+    $buffer = "Format: $format";
+    if($format == 'download_files') {
+        list($buffer, $format) = buildFileBuffer($files, $_GET['format'], $css, $studyTitle);
+    } else {
+        list($buffer, $format) = buildFileBuffer($results, $_GET['format'], $css, $studyTitle);
+    }
     $filename = "requested_data.".time().".$format";
 
     // set the headers
@@ -84,6 +110,21 @@
 
 function buildFileBuffer($data, $format, $css, $studyTitle) {
     switch($format) {
+    case 'download_files':
+        $buffer = '';
+        foreach($data as $file) {
+            global $downloadPath;
+            print "downloadPath: $downloadPath";
+            chdir($downloadPath);
+            $file = "./$file";
+            //print $file;
+            if(file_exists($file)) {
+                `tar rvf /var/www/neurodb/htdocs/foo.tar $file`;
+            }
+            $buffer .= "$file\n";
+        }
+        $format = 'txt';
+        break;
     case 'xls':
         $format = 'xls';
         require_once 'Spreadsheet/Excel/Writer.php';

diff --git a/htdocs/query_gui_data_loader.php b/htdocs/query_gui_data_loader.php
@@ -285,6 +285,10 @@
      // reference id, and send that to a popup
      $DB->insert("query_gui_downloadable_queries", array('query'=>$query));
      $queryID = $DB->lastInsertID;
+     $download = $_POST['download'];
+     if($download === 'execute') {
+         SendFilesToPackage($querySegments['selected_fields'], $query);
+     }
 
      $script .= "window.open('query_gui_data_download.php?queryID=$queryID&format=$_REQUEST[outputFormat]', 'query_download_window');";
 
@@ -293,6 +297,50 @@
 
 }
 
+function getFiles($cols, $query, $timestamp, $prefix="cbrain") {
+    $DB = Database::singleton();
+    $fileCols= array();
+    $lines=explode("\n",trim($cols));
+    foreach($lines as $field) {
+        $fileCol = $DB->pselectRow("SELECT IsFile, Name FROM parameter_type WHERE ParameterTypeID=:ptid", array("ptid" => $field));
+        if($fileCol['IsFile'] == true) {
+            $fileCols[] = ParameterTypeIDToFieldName($field);
+        }
+    }
+
+    // Strip off everything before from from the query that was generated above, then just re-add the file fields
+    // as determined above
+    $new_query = "SELECT " . join(',', $fileCols) . " " . substr($query, strpos($query, "FROM"));
+    $DB->select($new_query, $results);
+    $input = "";
+    $fp = fopen("/tmp/$prefix.$timestamp.txt", 'w');
+    foreach ($results as $row) {
+        foreach ($row as $key => $val) {
+            if(!empty($val)) {
+                fwrite($fp, $val . "\n");
+                $input .= $val . "\n";
+            }
+       }
+    }
+    fclose($fp);
+    return "/tmp/$prefix.$timestamp.txt";
+}
+
+function SendFilesToPackage($cols, $query) {
+    $DB = Database::singleton();
+    $user = User::singleton();
+    $timestamp = time();
+    $filelist = getFiles($cols,$query,$timestamp, "download");
+    $user = User::singleton();
+    chdir("../tools");
+    $cmd = sprintf("cat $filelist | ./%s %s.$timestamp > %s 2>&1 & echo $! >> %s", "package_files.sh", $user->getUsername(), "../logs/download.$timestamp", $filelist);
+    exec($cmd);
+    $cmd = "rm -f $filelist";
+    exec($cmd);
+    $DB->insert("query_gui_user_files", array("UserID" => $user->getData("ID"),
+        "filename" => $user->getUsername() . ".$timestamp.tar.gz"
+    ));
+}
 function printArray($array, $indent=""){
     while(list($key,$val)=each($array)){
         if(is_array($val)){
@@ -427,6 +475,7 @@ function treeToExpression(&$expression, &$tree, &$conditionals, $parentID=null)
 <form id='saveQueryForm' method='POST' action='query_gui_data_loader.php'>
 <textarea id='queryData' name='queryData'><?=$_POST['queryData']?></textarea>
 <input type='text' id='mode' name='mode'>
+<input type='text' id='download' name='download' />
 <input type='text' id='outputFormat' name='outputFormat'>
 <input type='submit'>
 </form>

diff --git a/php/libraries/NDB_Menu_Filter_download_files.class.inc b/php/libraries/NDB_Menu_Filter_download_files.class.inc
@@ -0,0 +1,111 @@
+<?
+require_once 'NDB_Menu_Filter.class.inc';
+
+class NDB_Menu_Filter_download_files extends NDB_Menu_Filter
+{
+    function _hasAccess()
+    {
+        $user =& User::singleton();
+        if (PEAR::isError($user)) {
+            return PEAR::raiseError("User Error: " .$user->getMessage());
+        }
+        return $user->hasPermission('download_files');
+    }
+
+    function _setupVariables()
+    {
+        $user =& User::singleton();
+
+        $this->query = " FROM query_gui_user_files f WHERE UserID=" . $user->getData("ID");
+
+        $this->columns = array('f.filename as File', 'f.downloadDate as QueryTime', 'f.md5sum as MD5', 'f.status as Status');
+        $this->order_by = 'downloadDate DESC';
+        $this->headers = array('Filename',
+                               'QueryTime',
+                               'MD5',
+                               'Status'
+        );
+        $this->validFilters = array('f.filename', 'f.status');
+        $this->formToFilter = array (
+                                    'Filename' =>  'f.filename'
+        );
+    }
+
+    function _setFilterForm()
+    {
+        $this->form->addElement('text', 'Filename', 'Filename:', array("size"=>9, "maxlength"=>11));
+    }
+
+    function _setDataTableRows($count)
+    {
+        $config = NDB_Config::singleton();
+        $db = Database::singleton();
+        $paths = $config->getSetting('paths');
+        $base = $paths['base'];
+        // print out
+        $x = 0;
+        foreach ($this->list as $item) {
+            //count column
+            $this->tpl_data['items'][$x][0]['value'] = $x + $count;
+
+            $file = false;
+            $md5 = false;
+
+            //print out data rows
+            $i = 1;
+            foreach ($item as $key => $val) {
+                $this->tpl_data['items'][$x][$i]['name'] = $key;
+                switch($key) {
+                    case 'File': $file = $val; break;
+                    case 'MD5': $md5 = $val; break;
+                    case 'Status':
+                        if($file && file_exists("$base/userdownloads/$file")) {
+                            if(!$md5) {
+                                $md5 = md5_file("$base/userdownloads/$file");
+                                // We're in the Status, MD5 was the previous column
+                                $this->tpl_data['items'][$x][$i-1]['value'] = $md5;
+                                $db->update("query_gui_user_files", array("status" => 'ready', 'md5sum' => $md5), array("filename" => $file));
+
+                            }
+                            $val = 'ready';
+                        } else {
+                            // If we're in this block, it means the file doesn't exist.
+                            // If there's no MD5 sum calculated yet, the file was never there. So it's packaging
+                            // If there is an MD5 sum but the file doesn't exist, it was deleted from the 
+                            // file system for space reasons, and it's "expired" for the user
+
+                            if(!$val || $val == 'ready') {
+                                if(!$md5) {
+                                    $db->update("query_gui_user_files", array("status" => 'packaging'), array("filename" => $file));
+                                    $val = 'packaging';
+                                } else {
+                                    $db->update("query_gui_user_files", array("status" => 'expired'), array("filename" => $file));
+                                    $val = 'expired';
+
+                                }
+                            }
+                        }
+                        break;
+                }
+
+                $this->tpl_data['items'][$x][$i]['value'] = $val;
+                $i++;
+            }
+            /*
+            $this->tpl_data['items'][$x][$i]['name'] = 'Status';
+            if($file && file_exists("$base/userdownloads/$file")) {
+                $this->tpl_data['items'][$x][$i]['value'] = 'Ready for download';
+                }
+            } else {
+                $this->tpl_data['items'][$x][$i]['value'] = 'Packaging files';
+                $db->update("query_gui_user_files", array("status" => 'packaging'), array("filename" => $file));
+            }
+            */
+
+            $x++;
+        }
+
+        return true;
+    }
+
+}