/**
  * Initialize all of the class variables and things required from the
  * REQUEST.
  *
  * @return none, but as a side-effect modifies class
  */
 function initialize()
 {
     ob_start('ob_gzhandler');
     $client = new NDB_Client();
     $client->makeCommandLine();
     $client->initialize();
     $this->caller =& NDB_Caller::singleton();
     $this->caller->setDataEntryType('Direct');
     if (empty($_REQUEST['key'])) {
         throw new Exception("Missing parameter", 403);
     }
     $this->key = $_REQUEST['key'];
     $DB = Database::singleton();
     $this->TestName = $DB->pselectOne("SELECT Test_name FROM participant_accounts\n            WHERE OneTimePassword=:key AND Status <> 'Complete'", array('key' => $this->key));
     $this->CommentID = $DB->pselectOne("SELECT CommentID FROM participant_accounts \n            WHERE OneTimePassword=:key AND Status <> 'Complete'", array('key' => $this->key));
     $this->NumPages = $DB->pselectOne("SELECT COUNT(*) FROM instrument_subtests WHERE Test_name=:TN", array('TN' => $this->TestName));
     if (empty($this->TestName) && empty($this->CommentID)) {
         throw new Exception("Data has already been submitted.", 403);
     }
     $pageNum = null;
     if (!empty($_REQUEST['pageNum'])) {
         $pageNum = $_REQUEST['pageNum'];
     }
     if ($pageNum === 'finalpage') {
         $this->Subtest = 'finalpage';
     } else {
         $this->Subtest = $DB->pselectOne("SELECT Subtest_name\n                FROM instrument_subtests\n                WHERE Test_name=:TN AND Order_number=:PN", array('TN' => $this->TestName, 'PN' => $pageNum));
     }
     $totalPages = $DB->pselectOne("SELECT COUNT(*)+1 from instrument_subtests WHERE Test_name=:TN", array('TN' => $this->TestName));
     $this->NextPageNum = $this->getNextPageNum($pageNum);
     $this->PrevPageNum = $this->getPrevPageNum($pageNum);
     $this->CommentID = $this->getCommentID();
     $this->tpl_data = array('nextpage' => $this->NextPageNum, 'prevpage' => $this->PrevPageNum, 'pageNum' => $pageNum ? $pageNum + 1 : 1, 'totalPages' => $totalPages, 'key' => $this->key);
 }

 function setUp()
 {
     $client = new NDB_Client();
     $client->makeCommandLine();
     $client->initialize();
     $this->DB = Database::singleton();
     $this->DB->setFakeTableData("test_names", array(array('ID' => 1, 'Test_name' => 'ActiveTestByAge', 'Full_name' => 'Active Test 1', 'Sub_group' => 1, 'IsDirectEntry' => 0), array('ID' => 2, 'Test_name' => 'ActiveTestByAge2', 'Full_name' => 'Active Test 2', 'Sub_group' => 1, 'IsDirectEntry' => 0), array('ID' => 3, 'Test_name' => 'InactiveTest', 'Full_name' => 'Inactive Test 1', 'Sub_group' => 1, 'IsDirectEntry' => 0), array('ID' => 4, 'Test_name' => 'ActiveTestByVisit', 'Full_name' => 'Active Test by Visit 1', 'Sub_group' => 1, 'IsDirectEntry' => 0), array('ID' => 5, 'Test_name' => 'ActiveTestByVisit2', 'Full_name' => 'Active Test by Visit 2', 'Sub_group' => 1, 'IsDirectEntry' => 0), array('ID' => 6, 'Test_name' => 'ActiveTestByFirstVisit', 'Full_name' => 'Active Test by First Visit 2', 'Sub_group' => 1, 'IsDirectEntry' => 0), array('ID' => 7, 'Test_name' => 'ActiveTestByNotFirstVisit', 'Full_name' => 'Active Test by Not First Visit 2', 'Sub_group' => 1, 'IsDirectEntry' => 0)));
     $this->DB->setFakeTableData("test_battery", array(array('ID' => 1, 'Test_name' => 'ActiveTestByAge', 'AgeMinDays' => 0, 'AgeMaxDays' => 100, 'Active' => 'Y', 'Stage' => 'Visit', 'SubprojectID' => 1, 'Visit_label' => null, 'CenterID' => null, 'firstVisit' => null), array('ID' => 2, 'Test_name' => 'ActiveTestByAge2', 'AgeMinDays' => 0, 'AgeMaxDays' => 100, 'Active' => 'Y', 'Stage' => 'Visit', 'SubprojectID' => 1, 'Visit_label' => null, 'CenterID' => '1', 'firstVisit' => null), array('ID' => 3, 'Test_name' => 'InactiveTest', 'AgeMinDays' => 0, 'AgeMaxDays' => 0, 'Active' => 'N', 'Stage' => 'Visit', 'SubprojectID' => 2, 'Visit_label' => 'V01', 'CenterID' => '1', 'firstVisit' => null), array('ID' => 4, 'Test_name' => 'ActiveTestByVisit', 'AgeMinDays' => 0, 'AgeMaxDays' => 0, 'Active' => 'Y', 'Stage' => 'Visit', 'SubprojectID' => 2, 'Visit_label' => 'V01', 'CenterID' => null, 'firstVisit' => null), array('ID' => 5, 'Test_name' => 'ActiveTestByVisit2', 'AgeMinDays' => 0, 'AgeMaxDays' => 0, 'Active' => 'Y', 'Stage' => 'Visit', 'SubprojectID' => 2, 'Visit_label' => 'V01', 'CenterID' => '1', 'firstVisit' => null), array('ID' => 6, 'Test_name' => 'ActiveTestByFirstVisit', 'AgeMinDays' => 0, 'AgeMaxDays' => 100, 'Active' => 'Y', 'Stage' => 'Visit', 'SubprojectID' => 1, 'Visit_label' => null, 'CenterID' => '1', 'firstVisit' => 'Y'), array('ID' => 7, 'Test_name' => 'ActiveTestByNotFirstVisit', 'AgeMinDays' => 0, 'AgeMaxDays' => 100, 'Active' => 'Y', 'Stage' => 'Visit', 'SubprojectID' => 1, 'Visit_label' => null, 'CenterID' => '1', 'firstVisit' => 'N')));
 }

 function testSetFakeData()
 {
     $client = new NDB_Client();
     $client->makeCommandLine();
     $client->initialize();
     $DB = Database::singleton();
     $DB->setFakeTableData("Config", array(0 => array('ID' => 99999, 'ConfigID' => '123456', 'Value' => 'FKE1234')));
     $allCandidates = $DB->pselect("SELECT * FROM Config", array());
     $this->assertEquals($allCandidates, array(0 => array('ID' => 99999, 'ConfigID' => 123456, 'Value' => 'FKE1234')));
 }

 /**
  * Validates the data which was passed in the request.
  *
  * @param string $method The HTTP method of the request
  * @param array  $data   The array-encode JSON posted to
  *                       the URL.
  */
 function __construct($method, $data = array())
 {
     $this->AllowedMethods = array('POST');
     $this->RequestData = $data;
     if (!in_array($method, $this->AllowedMethods)) {
         $this->header("HTTP/1.1 405 Method Not Allowed");
         $this->header("Allow: " . join(", ", $this->AllowedMethods));
         $this->safeExit(0);
     }
     $client = new \NDB_Client();
     // Bypass session handling because we're trying to authenticate a session
     $client->makeCommandLine();
     $client->initialize(__DIR__ . "/../../../project/config.xml");
     $this->HTTPMethod = $method;
     $this->handleRequest();
 }

<?php

/**
 * User: Stella
 * Date: 15-08-15
 *
 * Project Statistics - Updating Counts From Each LORIS
 */
set_include_path(get_include_path() . ":../php/libraries:");
require_once __DIR__ . "/../vendor/autoload.php";
$client = new NDB_Client();
$client->makeCommandLine();
$client->initialize('../project/config.xml');
$db =& Database::singleton();
$config = NDB_Config::singleton();
$date = date("m_d_Y");
$output_file = "project_statistics_{$date}.csv";
$fp = fopen($output_file, 'w');
echo "PROJECT STATISTICS SCRIPT - {$date}\n\n";
echo "Data can be found in {$output_file}.\n\n";
$headers = array('Project', 'Number of Scanning - Visits', 'Number of Sites', 'Variable Count', 'Number of instruments', 'total number of visits (for all candidates)', 'number of candidates', 'GB of imaging data (raw and processed)', '# of scans');
$counter = 0;
// Where project's statistics will be stored
$project_statistics = array();
// Project name
$projectname = $config->getSetting('title');
// Number of Scanning - Visits
$number_scanning_visits = $db->pselect("select count(*) from session where Scan_done='Y'", array());
// Number of Sites
$number_sites = $db->pselect("select count(*) from psc WHERE CenterID <>1", array());
// Variable Count

 *
 * Usage:
 *    php data_dictionary_builder.php
 *
 * PHP Version 5
 *
 * @category Behavioural
 * @package  Main
 * @author   Loris Team <[email protected]>
 * @license  Loris License
 * @link     https://github.com/aces/Loris
 */
set_include_path(get_include_path() . ":../project/libraries:../php/libraries:");
require_once __DIR__ . "/../vendor/autoload.php";
$configFile = "../project/config.xml";
$client = new NDB_Client();
$client->makeCommandLine();
$client->initialize($configFile);
$DB = Database::singleton();
// define which configuration file we're using for this installation
//Get the entries we already have in the DB
getColumns("Select Name, ParameterTypeID from parameter_type", $DB, $parameter_types);
//Delete in the parameter_type table relating to
//parameter_type_category.Type = 'Instrument', without affecting other entries.
//get parameter_type_category.Type ='Instrument' ParamenterTypeCategoryIDs
getColumn("SELECT ParameterTypeCategoryID\n        FROM parameter_type_category\n        WHERE Type = 'Instrument'", $DB, $instrumentParameterTypeCategoryIDs);
$instrumentParameterTypeCategoryIDString = implode(', ', $instrumentParameterTypeCategoryIDs);
//get all 'Instrument' ParameterTypeIDs
getColumn("SELECT ParameterTypeID\n        FROM parameter_type_category_rel\n        WHERE ParameterTypeCategoryID\n        IN ({$instrumentParameterTypeCategoryIDString})", $DB, $instrumentParameterTypeIDs);
$instrumentParameterTypeIDString = implode(', ', $instrumentParameterTypeIDs);
//delete all 'Instrument' entries from parameter_type_category_rel

<?php

/* This is used by the stats page to get the list of scorable columns for an
 * instrument via AJAX. It's used so that ScatterPlot-SVG.php can be run for
 * any scorable in an instrument, dynamically */
ini_set('default_charset', 'utf-8');
require_once "Database.class.inc";
require_once 'NDB_Config.class.inc';
require_once 'NDB_Client.class.inc';
$config =& NDB_Config::singleton();
$client = new NDB_Client();
$client->makeCommandLine();
$client->initialize();
require_once "Utility.class.inc";
$cols = Utility::getScoreColsForInstrument($_REQUEST['instrument']);
if (strrpos($_REQUEST['instrument'], "_proband") === false) {
    print "Candidate_Age\n";
}
foreach ($cols as $val) {
    print "{$val}\n";
}

<?php

$user =& User::singleton();
if (!$user->hasPermission('dataquery_view')) {
    header("HTTP/1.1 403 Forbidden");
    exit;
}
require_once __DIR__ . '/../../../vendor/autoload.php';
$client = new NDB_Client();
$client->makeCommandLine();
$client->initialize(__DIR__ . "/../../../project/config.xml");
$cdb = CouchDB::singleton();
$category = $_REQUEST['category'];
$results = $cdb->queryView("DQG-2.0", "datadictionary", array("reduce" => "false", "startkey" => "[\"{$category}\"]", "endkey" => "[\"{$category}\", \"ZZZZZZZZ\"]"));
print json_encode($results);

 * @license  http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
 * @link     https://www.github.com/aces/Loris/
 */
if (isset($_SERVER['HTTP_ORIGIN'])) {
    header("Access-Control-Allow-Origin: " . $_SERVER['HTTP_ORIGIN']);
    header("Access-Control-Allow-Credentials: true");
}
set_include_path(get_include_path() . ":../project/libraries:../php/libraries:");
require_once __DIR__ . "/../vendor/autoload.php";
ini_set('default_charset', 'utf-8');
ob_start('ob_gzhandler');
// Create an output buffer to capture console output, separately from the
// gzip handler.
ob_start();
// load the client
$client = new NDB_Client();
if ($client->initialize() == false) {
    return false;
}
// require additional libraries
$TestName = isset($_REQUEST['test_name']) ? $_REQUEST['test_name'] : 'dashboard';
$subtest = isset($_REQUEST['subtest']) ? $_REQUEST['subtest'] : '';
// make local instances of objects
$config =& NDB_Config::singleton();
//--------------------------------------------------
/**
 * Extracts a parameter from request in a safe way,
 * and sets the $tpl_data to said request. If request does
 * not contain parameter, will set the smarty variable to
 * empty
 *

 *  @package  Document Repository
 *  @author   Dave MacFarlane <[email protected]>
 *  @license  Loris license
 *  @link     https://github.com/aces/Loris-Trunk
 *
 */
$user =& User::singleton();
if (!$user->hasPermission('document_repository_view') && !$user->hasPermission('document_repository_delete')) {
    header("HTTP/1.1 403 Forbidden");
    exit;
}
// Load config file and ensure paths are correct
set_include_path(get_include_path() . ":" . __DIR__ . "/../project/libraries:" . __DIR__ . "/../php/libraries");
// Ensures the user is logged in, and parses the config file.
require_once "NDB_Client.class.inc";
$client = new NDB_Client();
$client->initialize("../project/config.xml");
// Checks that config settings are set
$config =& NDB_Config::singleton();
$File = $_GET['File'];
// Make sure that the user isn't trying to break out of the $path by
// using a relative filename.
// No need to check for '/' since all downloads are relative to $basePath
if (strpos("..", $File) !== false) {
    error_log("ERROR: Invalid filename");
    header("HTTP/1.1 400 Bad Request");
    exit(4);
}
$FullPath = __DIR__ . "/../user_uploads/{$File}";
if (!file_exists($FullPath)) {
    error_log("ERROR: File {$FullPath} does not exist");

 * that follows the user in Loris.
 *
 * PHP Version 5
 *
 * @category Behavioural
 * @package  Loris
 * @author   Loris Team <[email protected]>
 * @license  http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
 * @link     https://www.github.com/aces/Loris/
 */
set_include_path(get_include_path() . ":../project/libraries:../php/libraries:");
require_once __DIR__ . '/../vendor/autoload.php';
ini_set('default_charset', 'utf-8');
ob_start('ob_gzhandler');
require_once "NDB_Client.class.inc";
$client = new NDB_Client();
$client->initialize();
$config =& NDB_Config::singleton();
$paths = $config->getSetting('paths');
// create user object
$user =& User::singleton();
if (PEAR::isError($user)) {
    die("Error creating user object: " . $user->getMessage());
}
$tpl_data['userID'] = $user->getData('UserID');
// set permissions
if ($user->hasPermission('bvl_feedback')) {
    $tpl_data['has_permission'] = true;
}
// create candidate object if we have a candID
if (!empty($_REQUEST['candID'])) {