/**
* Add file in given feed
* @return bool
*/
public static function add($feedID, $files, $ssh_connection)
{
// set permissions with the ssh connection
// get feed path
$mapper = new Mapper('Feed');
$mapper->get($feedID);
$resultsFeed = $mapper->get();
$mapper = new Mapper('User');
$mapper->get($resultsFeed['Feed'][0]->user_id);
$resultsUser = $mapper->get();
// target directory
$dir = CHRIS_USERS . '/' . $resultsUser['User'][0]->username . '/file_browser/' . $resultsFeed['Feed'][0]->name . '-' . $resultsFeed['Feed'][0]->id . '/';
$ssh_connection->exec('chmod 777 ' . $dir);
foreach ($files as $key => $value) {
$target_path = $dir . basename($value['name']);
if (move_uploaded_file($value['tmp_name'], $target_path)) {
// all good, set permissions correctly
// not through ssh connection, do it as chris
exec('chmod 775 ' . $target_path);
} else {
// oops.... something went wrong
return $value['error'];
}
$ssh_connection->exec('chmod 755 ' . $dir);
}
// all files uploaded successfully
return 0;
}
/**
* Validate a token. Returns the result and deletes the token if valid.
*
* @param string $token The token
* @return boolean
*/
public static function validate($token)
{
$tokenMapper = new Mapper('Token');
$tokenMapper->filter('value=(?)', $token);
$tokenResults = $tokenMapper->get();
if (count($tokenResults['Token']) == 0) {
return false;
}
// we found the token
Mapper::delete($tokenResults['Token'][0], $tokenResults['Token'][0]->id);
return true;
}
/**
* Get username from user id.
* @param int $userid user ID
* @return string username
*/
private static function _getUsername($userid)
{
// get user name
$userMapper = new Mapper('User');
$userMapper->filter('id = (?)', $userid);
$userResult = $userMapper->get();
$username = "******";
if (count($userResult['User']) == 1) {
$username = $userResult['User'][0]->username;
}
return $username;
}
require_once joinPaths(CHRIS_MODEL_FOLDER, 'user.model.php');
// main function
$shortopts = "u:z:";
$options = getopt($shortopts);
$username = '';
if (isset($options['u'])) {
$username = $options['u'];
}
$zipfile = '';
if (isset($options['z'])) {
$zipfile = $options['z'];
}
// Get username
$userMapper = new Mapper('User');
$userMapper->filter('username = (?)', $username);
$userResult = $userMapper->get();
$emailTo = '';
if (count($userResult['User']) != 0) {
$emailTo = $userResult['User'][0]->email;
}
// Build message and link:
$link = CHRIS_URL . "/index.php?";
$link .= "launch_plugin=1";
$link .= "&plugin=zip";
$feedname = "ChRIS_Pushed";
$link .= "&feedname={$feedname}";
$link .= "&status=0";
$link .= "&status_step=100";
$command = "--input={$zipfile} --unzip";
$link .= "&ncommand=" . urlencode($command);
$message = "Please click on the following link to create a new feed for this data: " . PHP_EOL;
$patientMapper = new Mapper('Data_Patient');
$patientMapper->ljoin('Patient', 'Patient.id = Data_Patient.patient_id');
$patientMapper->filter('Data_Patient.data_id = (?)', $dataResult['Data'][0]->id);
$patientResult = $patientMapper->get();
// create feed patient directories
// mkdir if dir doesn't exist
// create folder if doesnt exists
$datadirname = $output_directory . '/' . $patientResult['Patient'][0]->uid . '-' . $patientResult['Patient'][0]->id;
if (!is_dir($datadirname)) {
mkdir($datadirname);
}
// study directory
// get study description
$studyMapper = new Mapper('Study');
$studyMapper->filter('uid = (?)', $process_file['StudyInstanceUID'][0]);
$studyResult = $studyMapper->get();
$study_dir_name = formatStudy($studyResult['Study'][0]->date, $studyResult['Study'][0]->age, $studyResult['Study'][0]->description) . '-' . $studyResult['Study'][0]->id;
$studydirname = $datadirname . '/' . $study_dir_name;
if (!is_dir($studydirname)) {
mkdir($studydirname);
}
// create data soft links
$targetbase = CHRIS_DATA . '/' . $patientResult['Patient'][0]->uid . '-' . $patientResult['Patient'][0]->id;
$series_dir_name = $dataResult['Data'][0]->description . '-' . $dataResult['Data'][0]->name;
$seriesdirnametarget = $targetbase . '/' . $study_dir_name . '/' . $series_dir_name . '-' . $dataResult['Data'][0]->id;
$seriesdirnamelink = $datadirname . '/' . $study_dir_name . '/' . $series_dir_name . '-' . $dataResult['Data'][0]->id;
if (!is_link($seriesdirnamelink)) {
// create sof link
symlink($seriesdirnametarget, $seriesdirnamelink);
}
$waiting = false;
public static function AddStudy(&$db, &$process_file, &$study_chris_id, &$study_description)
{
$db->lock('study', 'WRITE');
// Does data exist: SeriesInstanceUID
if (array_key_exists('StudyInstanceUID', $process_file)) {
// does study exist??
$studyMapper = new Mapper('Study');
$studyMapper->filter('uid = (?)', $process_file['StudyInstanceUID'][0]);
$studyResult = $studyMapper->get();
// if study doesn't exist, create it
if (count($studyResult['Study']) == 0) {
// create object
// create data model
$studyObject = new Study();
//
// get data uid
//
$studyObject->uid = $process_file['StudyInstanceUID'][0];
//
// get data name (series description)
//
if (array_key_exists('StudyDescription', $process_file)) {
$studyObject->description = sanitize($process_file['StudyDescription'][0]);
} else {
$studyObject->description = 'NoStudyDescription';
}
if (array_key_exists('Modality', $process_file)) {
$studyObject->modality = sanitize($process_file['Modality'][0]);
} else {
$studyObject->modality = 'NoModality';
}
if (array_key_exists('StudyDate', $process_file)) {
$studyObject->date = PACS::getDate($process_file);
}
$studyObject->age = PACS::getAge($process_file);
$studyObject->location = PACS::getLocation($process_file);
$study_description = formatStudy($studyObject->date, $studyObject->age, $studyObject->description);
$study_chris_id = Mapper::add($studyObject);
} else {
// Content to be updated
if ($studyResult['Study'][0]->age == -1) {
//
// get data name (series description)
//
if (array_key_exists('StudyDescription', $process_file)) {
$studyResult['Study'][0]->description = sanitize($process_file['StudyDescription'][0]);
} else {
$studyResult['Study'][0]->description = 'NoStudyDescription';
}
if (array_key_exists('Modality', $process_file)) {
$studyResult['Study'][0]->modality = sanitize($process_file['Modality'][0]);
} else {
$studyResult['Study'][0]->modality = 'NoModality';
}
$studyResult['Study'][0]->date = PACS::getDate($process_file);
$studyResult['Study'][0]->age = PACS::getAge($process_file);
$studyResult['Study'][0]->location = PACS::getLocation($process_file);
$study_description = formatStudy($studyResult['Study'][0]->date, $studyResult['Study'][0]->age, $studyResult['Study'][0]->description);
$study_chris_id = $studyResult['Study'][0]->id;
Mapper::update($studyResult['Study'][0], $studyResult['Study'][0]->id);
} else {
$study_chris_id = $studyResult['Study'][0]->id;
$study_description = formatStudy($studyResult['Study'][0]->date, $studyResult['Study'][0]->age, $studyResult['Study'][0]->description);
}
}
} else {
echo 'Study UID not provided in DICOM file' . PHP_EOL;
// finish data table lock
$db->unlock();
return 0;
}
// finish data table lock
$db->unlock();
return 1;
}
public static function status($feedid, $status, $op)
{
// get $db instance
$db = DB::getInstance();
$db->lock('feed', 'WRITE');
// grab the feed
$feedResult = Mapper::getStatic('Feed', $feedid);
if (count($feedResult['Feed']) == 0) {
$db->unlock();
die('Invalid feed id.');
}
# grab old status
$old_status = $feedResult['Feed'][0]->status;
$type = gettype($status);
echo "Performing '{$op}' with value '{$status}' on current status '{$old_status}'\n";
if ($op == 'inc') {
// increasing mode
echo "Increasing status of feed {$feedid} by {$status}... ";
# increase status
$status = $old_status + $status;
}
if ($op == 'set') {
// set mode
if ($old_status >= $status || $status > 100) {
$db->unlock();
die("Ignoring setting the status since the old status {$old_status} >= the new status {$status} or the old status >= 100.\n");
} else {
echo "Setting status of feed {$feedid} to {$status}... ";
}
}
echo "status now {$status}.\n";
# clamp the addition
if ($status >= 100) {
$status = 100;
$startTime = $feedResult['Feed'][0]->time;
$endTime = microtime(true);
$duration = $endTime - $startTime;
$feedResult['Feed'][0]->time = $endTime;
$feedResult['Feed'][0]->duration = $duration;
}
# push to database
$feedResult['Feed'][0]->status = $status;
Mapper::update($feedResult['Feed'][0], $feedid);
$db->unlock();
# update related shared feeds
$relatedMapper = new Mapper('Feed');
$relatedMapper->join('Meta', 'Meta.target_id = Feed.id')->filter('Meta.name = (?)', 'root_id')->filter('Meta.value = (?)', $feedResult['Feed'][0]->id)->filter('Feed.id != (?)', $feedResult['Feed'][0]->id);
$relatedResult = $relatedMapper->get();
foreach ($relatedResult['Feed'] as $key => $value) {
$relatedResult['Feed'][$key]->time = $feedResult['Feed'][0]->time;
$relatedResult['Feed'][$key]->duration = $feedResult['Feed'][0]->duration;
$relatedResult['Feed'][$key]->status = $feedResult['Feed'][0]->status;
Mapper::update($relatedResult['Feed'][$key], $relatedResult['Feed'][$key]->id);
}
# send email if status == 100
if ($status == 100) {
// user's email
$userMapper = new Mapper('User');
$userMapper->filter('user.id = (?)', $feedResult['Feed'][0]->user_id);
$userResult = $userMapper->get();
// if nothing in DB yet, return -1
if (count($userResult['User']) > 0) {
$subject = "ChRIS2 - " . $feedResult['Feed'][0]->plugin . " plugin finished";
$message = "Hello " . $userResult['User'][0]->username . "," . PHP_EOL . PHP_EOL;
$message .= "Your results are available at:" . PHP_EOL . PHP_EOL;
$dirRoot = joinPaths(CHRIS_USERS, $userResult['User'][0]->username, $feedResult['Feed'][0]->plugin, $feedResult['Feed'][0]->name . '-' . $feedResult['Feed'][0]->id);
$dataDir = array_diff(scandir($dirRoot), array('..', '.'));
foreach ($dataDir as $dir) {
$mailFilePath = $dirRoot . '/' . $dir . '/_chrisRun_/' . 'chris.mail';
if (file_exists($mailFilePath)) {
$mailContents = file_get_contents($mailFilePath);
$message .= $dirRoot . '/' . $dir . PHP_EOL . $mailContents . PHP_EOL . PHP_EOL;
} else {
$message .= $dirRoot . '/' . $dir . PHP_EOL . PHP_EOL;
}
}
$message .= "Thank you for using ChRIS.";
echo "Sending email to " . $userResult['User'][0]->email . " since the status is '{$status}'%.\n";
// get user email address
email(CHRIS_PLUGIN_EMAIL_FROM, $userResult['User'][0]->email, $subject, $message);
}
}
}
public function testGet()
{
// get a patient by id
$patientObject = new Patient();
$patientObject->id = 2;
$patientObject->name = 'Rannou';
$patientObject->dob = '1987-03-27';
$patientObject->sex = 'M';
$patientObject->uid = 'CH156525;';
$patientObject2 = new Patient();
$patientObject2->id = 2;
$patientObject2->name = 'Rannou';
$patientObject2->dob = '1987-03-27';
$patientObject2->sex = 'M';
$patientObject2->uid = 'CH156525;';
$patientMapper = new Mapper($patientObject);
$patientResult = $patientMapper->get(2);
// should be equal
//$this->assertTrue($patientResult['Patient'][0]->equals($patientObject2) == True);
$patientMapper2 = new Mapper('Patient');
$patientResult2 = $patientMapper2->get(-3);
// should return nothing
$this->assertTrue(count($patientResult2['Patient']) == 0);
// get all
$patientMapper3 = new Mapper($patientObject);
$patientMapper3->filter('AND', '', 0);
$patientResult3 = $patientMapper3->get();
// should return 6 patients
$this->assertTrue(count($patientResult3['Patient']) == 6);
}
$processLog .= 'agemin: '. $input.PHP_EOL;
$mapper->filter('study.age <= (?)', $input);
$processLog .= 'agemax: '. $input.PHP_EOL; */
/* $mapper->filter('study.date >= (?)', $input);
$processLog .= 'datemin: '. $input.PHP_EOL;
$mapper->filter('study.date <= (?)', $input);
$processLog .= 'datemax: '. $input.PHP_EOL; */
}
$fh = fopen($logFile, 'a') or die("can't open file");
fwrite($fh, $processLog);
fclose($fh);
$processLog = '=======================================' . PHP_EOL;
$processLog .= date('Y-m-d h:i:s') . ' ---> Process results...' . PHP_EOL;
$results = $mapper->get();
if (count($results['Data']) >= 1) {
foreach ($results['Data'] as $key => $value) {
$processLog .= $results['Patient'][$key]->id . PHP_EOL;
// create patient directory
$fs_location = $results['Patient'][$key]->uid . '-' . $results['Patient'][$key]->id;
$patientdir = $output_dir . $fs_location;
// create study directory
$fs_location .= '/' . formatStudy($results['Study'][$key]->date, $results['Study'][$key]->age, $results['Study'][$key]->description) . '-' . $results['Study'][$key]->id;
$studydir = $output_dir . $fs_location;
// create data symlink
// loop through results and create links
$processLog .= date('Y-m-d h:i:s') . ' Creates soft link for Patient' . PHP_EOL;
// create data soft links
$name = '';
if (file_exists(CHRIS_DATA . '/' . $fs_location . '/' . $value->description . '-' . $value->name . '-' . $value->id)) {
$targetbase = CHRIS_DATA . '/' . $patientResult['Patient'][0]->uid . '-' . $patientResult['Patient'][0]->id;
$series_dir_name = $dataResult['Data'][0]->description . '-' . $dataResult['Data'][0]->name;
$seriesdirnametarget = $targetbase . '/' . $study_dir_name . '/' . $series_dir_name . '-' . $dataResult['Data'][0]->id;
$seriesdirnamelink = $datadirname . '/' . $study_dir_name . '/' . $series_dir_name . '-' . $dataResult['Data'][0]->id;
if (file_exists($seriesdirnametarget)) {
if (!is_link($seriesdirnamelink)) {
// create sof link
symlink($seriesdirnametarget, $seriesdirnamelink);
}
} else {
$dataLog .= "ERROR: Directory does not exist: " . $seriesdirnametarget . PHP_EOL;
}
// update feed status?
$fh = fopen($logFile, 'a') or die("can't open file");
fwrite($fh, $dataLog);
fclose($fh);
$waiting = false;
} else {
sleep(2);
}
}
// update status
$counter++;
}
// update feed status in db
$feedMapper = new Mapper('Feed');
$feedMapper->filter('id = (?)', $feed_chris_id);
$feedResult = $feedMapper->get();
$feedResult['Feed'][0]->status = 99;
Mapper::update($feedResult['Feed'][0], $feedResult['Feed'][0]->id);
exit(0);
public static function getTagsList()
{
$n = new Template('tags_list.html');
$tagMapper = new Mapper('Tag');
$tagMapper->filter('user_id=(?)', $_SESSION['userid']);
$tagresults = $tagMapper->get();
$tags = '';
foreach ($tagresults['Tag'] as $key => $value) {
$tags .= '<option value="' . $value->name . '" data-backgroundcolor="' . $value->color . '" data-color="' . invertColor($value->color) . '">' . $value->name . '</option>';
}
$n->replace('TAGS_LIST', $tags);
return $n;
}
// delete the temp file
unlink($study_directory . '/' . $entry2);
}
}
}
closedir($handle2);
// delete directory
$logFile .= 'delete: ' . $study_directory . PHP_EOL;
rmdir($study_directory);
}
// add warning if we didn't receive all the expected files
// todo: all queries at once
foreach ($received as $key => $value) {
$dataMapper = new Mapper('Data');
$dataMapper->filter('id = (?)', $value);
$dataResult = $dataMapper->get();
if ($dataResult['Data'][0]->status != $dataResult['Data'][0]->nb_files) {
$logFile .= 'WARNING => DATA ID : ' . $dataResult['Data'][0]->id . '(' . $dataResult['Data'][0]->status . '/' . $dataResult['Data'][0]->nb_files . ')' . $entry . PHP_EOL;
// update db to unlock plugin
if ($dataResult['Data'][0]->nb_files == -1) {
$dataResult['Data'][0]->nb_files = $dataResult['Data'][0]->status;
} else {
$dataResult['Data'][0]->status = min($dataResult['Data'][0]->status, $dataResult['Data'][0]->nb_files);
$dataResult['Data'][0]->nb_files = $dataResult['Data'][0]->status;
}
Mapper::update($dataResult['Data'][0], $dataResult['Data'][0]->id);
}
}
sendEmail($process_file, $datadirname, $emailTo, $link);
echo $logFile;
return;
/**
* Set a user email address.
*
* @param string $uid
* @param string $email
*/
public static function setEmail($uid, $email)
{
$userMapper = new Mapper('User');
$userMapper->filter('id=(?)', $uid);
$userResults = $userMapper->get();
// if user exist, return its id
if (isset($userResults['User'][0])) {
// update email address
$userResults['User'][0]->email = $email;
Mapper::update($userResults['User'][0], $uid);
}
}
