/**
* Returns the path under which minc files are located in this Loris
* install.
*
* @return string Path which contains MINC files
*/
function getMincLocation()
{
$config =& NDB_Config::singleton();
$paths = $config->getSetting('paths');
$minc_path = $paths['mincPath'];
return $minc_path;
}
/**
* Get the last changed log file using in the
* $paths['base'] . "/" . $paths['log']."/MRI_upload" directory
* @return String latest log file
*/
function getLatestLogFile()
{
$config = NDB_Config::singleton();
$paths = $config->getSetting('paths');
///////////////////////////////////////////////////////////////////////////
///////////////////get the path from the config file///////////////////////
///////////////////////////////////////////////////////////////////////////
if (empty($paths)) {
print "config setting is missing";
error_log("ERROR: Config settings are missing");
}
///////////////////////////////////////////////////////////////////////////
//////////////////////Get the directory name///////////////////////////////
///////////////////////////////////////////////////////////////////////////
$log_directory = $paths['base'] . "/" . $paths['log'] . "/MRI_upload";
//print "log directory " . $log_directory . "<BR>";
//get the last file modified
///////////////////////////////////////////////////////////////////////////
////////////////find the file last changed/////////////////////////////////
///////////////////////////////////////////////////////////////////////////
$files = glob($log_directory . "/*MRI_upload*");
$files = array_combine($files, array_map("filemtime", $files));
arsort($files);
$data_source_file = key($files);
if (!file_exists($data_source_file)) {
print "File doesn't exist";
}
return $data_source_file;
}
/**
* Handles the media upload process
*
* @throws DatabaseException
*
* @return void
*/
function uploadFile()
{
$db =& Database::singleton();
$config = NDB_Config::singleton();
$user =& User::singleton();
if (!$user->hasPermission('media_write')) {
header("HTTP/1.1 403 Forbidden");
exit;
}
// Validate media path and destination folder
$mediaPath = $config->getSetting('paths')['mediaPath'];
if (!isset($mediaPath)) {
showError("Error! Media path is not set in Loris Settings!");
exit;
}
if (!file_exists($mediaPath)) {
showError("Error! The upload folder '{$mediaPath}' does not exist!");
exit;
}
// Make sure folder is writable
chmod($mediaPath, 0777);
// Process posted data
$pscid = isset($_POST['pscid']) ? $_POST['pscid'] : null;
$visit = isset($_POST['visit_label']) ? $_POST['visit_label'] : null;
$instrument = isset($_POST['instrument']) ? $_POST['instrument'] : null;
$site = isset($_POST['for_site']) ? $_POST['for_site'] : null;
$dateTaken = isset($_POST['date_taken']) ? $_POST['date_taken'] : null;
$comments = isset($_POST['comments']) ? $_POST['comments'] : null;
// If required fields are not set, show an error
if (!isset($_FILES) || !isset($pscid) || !isset($visit) || !isset($site)) {
showError("Please fill in all required fields!");
return;
}
$fileName = $_FILES["file"]["name"];
$fileType = $_FILES["file"]["type"];
$userID = $user->getData('UserID');
$sessionID = $db->pselectOne("SELECT s.ID as session_id FROM candidate c " . "LEFT JOIN session s USING(CandID) WHERE c.PSCID = :v_pscid AND " . "s.Visit_label = :v_visit_label AND s.CenterID = :v_center_id", ['v_pscid' => $pscid, 'v_visit_label' => $visit, 'v_center_id' => $site]);
if (!isset($sessionID) || count($sessionID) < 1) {
showError("Error! A session does not exist for candidate '{$pscid}'' " . "and visit label '{$visit}'.");
return;
}
// Build insert query
$query = ['session_id' => $sessionID, 'instrument' => $instrument, 'date_taken' => $dateTaken, 'comments' => $comments, 'file_name' => $fileName, 'file_type' => $fileType, 'data_dir' => $mediaPath, 'uploaded_by' => $userID, 'hide_file' => 0, 'date_uploaded' => date("Y-m-d H:i:s")];
if (move_uploaded_file($_FILES["file"]["tmp_name"], $mediaPath . $fileName)) {
$db->insert('media', $query);
} else {
showError("Could not upload the file. Please try again!");
}
}
<?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
function run()
{
$config = $this->CouchDB->replaceDoc('Config:BaseConfig', $this->Config);
print "Updating Config:BaseConfig: {$config}";
// Run query
$demographics = $this->SQLDB->pselect($this->_generateQuery(), array());
$this->CouchDB->beginBulkTransaction();
$config_setting = NDB_Config::singleton();
foreach ($demographics as $demographics) {
$id = 'Demographics_Session_' . $demographics['PSCID'] . '_' . $demographics['Visit_label'];
$demographics['Cohort'] = $this->_getSubproject($demographics['SubprojectID']);
unset($demographics['SubprojectID']);
if (isset($demographics['ProjectID'])) {
$demographics['Project'] = $this->_getProject($demographics['ProjectID']);
unset($demographics['ProjectID']);
}
if ($config_setting->getSetting("useFamilyID") === "true") {
$familyID = $this->SQLDB->pselectOne("SELECT FamilyID FROM family\n WHERE CandID=:cid", array('cid' => $demographics['CandID']));
if (!empty($familyID)) {
$this->Dictionary["FamilyID"] = array('Description' => 'FamilyID of Candidate', 'Type' => "int(6)");
$demographics['FamilyID'] = $familyID;
$familyFields = $this->SQLDB->pselect("SELECT candID as Family_ID,\n Relationship_type as Relationship_to_candidate\n FROM family\n WHERE FamilyID=:fid AND CandID<>:cid", array('fid' => $familyID, 'cid' => $demographics['CandID']));
$num_family = 1;
if (!empty($familyFields)) {
foreach ($familyFields as $row) {
//adding each sibling id and relationship to the file
$this->Dictionary["Family_CandID" . $num_family] = array('Description' => 'CandID of Family Member ' . $num_family, 'Type' => "varchar(255)");
$this->Dictionary["Relationship_type_Family" . $num_family] = array('Description' => 'Relationship of candidate to Family Member ' . $num_family, 'Type' => "enum('half_sibling','full_sibling','1st_cousin')");
$demographics['Family_CandID' . $num_family] = $row['Family_ID'];
$demographics['Relationship_type_Family' . $num_family] = $row['Relationship_to_candidate'];
$num_family += 1;
}
}
}
}
$success = $this->CouchDB->replaceDoc($id, array('Meta' => array('DocType' => 'demographics', 'identifier' => array($demographics['PSCID'], $demographics['Visit_label'])), 'data' => $demographics));
print "{$id}: {$success}\n";
}
$this->_updateDataDict();
$this->CouchDB->replaceDoc('DataDictionary:Demographics', array('Meta' => array('DataDict' => true), 'DataDictionary' => array('demographics' => $this->Dictionary)));
print $this->CouchDB->commitBulkTransaction();
}
/**
* Constructor function. Instantiates references to database and
* config class.
*
* @return VisitWindowPopulator
*/
function __construct()
{
$this->DB = Database::singleton();
$this->Config = NDB_Config::singleton();
}
/**
* Get the excluded instruments from the config file
*
* @return Array List of instruments to be skipped
*/
function getExcludedInstruments()
{
// Get the abbreviated instruments
$config =& NDB_Config::singleton();
$excluded_instruments = $config->getSetting('excluded_instruments');
$ex_instruments = array();
foreach ($excluded_instruments as $instruments) {
foreach (Utility::asArray($instruments) as $instrument) {
$ex_instruments[$instrument] = $instrument;
}
}
return $ex_instruments;
}
/**
* Updates DQT with the new data
*
* @param array $data Candidate data to be updated
* @param array $ScanTypes All selected scan types in the database
*
* @return void
*/
function updateCandidateDocs($data, $ScanTypes)
{
foreach ($data as $row) {
$doc = $row;
$identifier = array($row['PSCID'], $row['Visit_label']);
$docid = 'MRI_Files:' . join($identifier, '_');
unset($doc['PSCID']);
unset($doc['Visit_label']);
unset($doc['SessionID']);
$success = $this->CouchDB->replaceDoc($docid, array('Meta' => array('DocType' => 'mri_data', 'identifier' => $identifier), 'data' => $doc));
print $docid . ": " . $success . "\n";
$config = NDB_Config::singleton();
$paths = $config->getSetting('paths');
foreach ($ScanTypes as $Scan) {
// This isn't very efficient to get the document a second time, but
// we need the rev for adding the attachments. This whole section
// should be optimized/cleaned up. For now it's just a hack to get
// the data into CouchDB, it isn't very clean.
// This should all be done using a single multipart request
// eventually.
$latestDoc = $this->CouchDB->getDoc($docid);
$fileName = $doc['Selected_' . $Scan['ScanType']];
$fullPath = $paths['mincPath'] . $fileName;
if (file_exists($fullPath)) {
if (!empty($fileName)) {
$toUpload = null;
if (!empty($latestDoc['_attachments'])) {
if (isset($latestDoc['_attachments'][$fileName])) {
$latest_doc = $latestDoc['_attachments'][$fileName];
$size = $latest_doc['length'];
if ($size != filesize($fullPath)) {
// File has been modified, upload it.
$toUpload = $fileName;
}
} else {
// This attachment not been uploaded - ever
$toUpload = $fileName;
}
} else {
// No current attachments, so this file has not
// been uploaded
$toUpload = $fileName;
}
if (!empty($toUpload)) {
$data = file_get_contents($fullPath);
print "Adding {$fileName} to {$docid}\n";
$latest = $latestDoc['_rev'];
$rev = $docid . '/' . $fileName . '?rev=' . $latest;
$output = $this->CouchDB->_postRelativeURL($rev, $data, 'PUT', 'application/x-minc');
}
}
} else {
print "****COULD NOT FIND {$fullPath} TO ADD TO {$docid}***\n";
}
}
}
return;
}
/**
* This create the relations between the file and the candidates
* that have values inserted.
*
* @param object $fileToUpload The object containing the $_FILES
* and the $_POST values.
*
* @return void
*/
function createCandidateFileRelations(&$fileToUpload)
{
$config = NDB_Config::singleton();
$genomic_data_dir = $config->getSetting('GenomicDataPath');
$DB =& Database::singleton();
$f = fopen($genomic_data_dir . 'genomic_uploader/' . $fileToUpload->file_name, "r");
if ($f) {
$stmt_prefix = 'INSERT IGNORE INTO genomic_candidate_files_rel
(CandID, GenomicFileID) VALUES ';
$stmt = '';
$line = fgets($f);
fclose($f);
$headers = explode(',', $line);
array_shift($headers);
$rows = array();
foreach ($headers as $pscid) {
$pscid = trim($pscid);
$row = "(\n (select CandID from candidate where PSCID = '{$pscid}'),\n {$fileToUpload->GenomicFileID}\n )";
array_push($rows, $row);
}
$stmt .= join(',', $rows);
try {
$prep = $DB->prepare($stmt_prefix . $stmt);
$result = $DB->execute($prep, array(), array('nofetch' => true));
} catch (DatabaseException $e) {
die(json_encode(array('message' => 'File registration failed', 'progress' => 100, 'error' => true)));
}
} else {
die(json_encode(array('message' => 'Beta value file can`t be opened', 'progress' => 100, 'error' => true)));
}
reportProgress(50, "Creating file-candidate relations");
}