/**
*
* @param Picture $picture_
* @throws InvalidArgumentException
*/
public function updatePicture(Picture $picture_)
{
try {
if (isset($this->table) && is_null($this->table)) {
throw new InvalidArgumentException('Attribute "table" can\'t be NULL !');
}
if (isset($this->id) && !is_null($this->id)) {
$where = 'id = ' . $this->id;
}
//Existance test
$picture = $this->selectPicture();
if (!emptyObjectMethod($picture)) {
$picture = $this->selectPicture();
$path = $picture->getPath();
$title = $picture->getTitle();
$ext = $picture->getExtension();
if (file_exists(UPLOAD_PATH . $path . $title . '.' . $ext)) {
if (!is_null($picture_->getTitle()) && $title !== $picture_->getTitle()) {
if (!rename(UPLOAD_PATH . $path . $title . '.' . $ext, UPLOAD_PATH . $path . $picture_->getTitle() . '.' . $ext)) {
throw new Exception('A problem occurred when renaming !');
}
}
}
} else {
throw new Exception('Picture doesn\'t exist !');
}
return parent::update($this->table, $picture_, $where);
} catch (InvalidArgumentException $e) {
print $e->getMessage();
exit;
} catch (Exception $e) {
print $e->getMessage();
exit;
}
}
/**
*
* @param Tag $tag_
* @throws InvalidArgumentException
*/
public function updateTag(Tag $tag_)
{
try {
if (is_null($this->table)) {
throw new InvalidArgumentException('Attribute "table" can\'t be NULL !');
}
if (isset($this->id) && !is_null($this->id)) {
$where = 'id = ' . $this->id;
}
$tagMapper = new TagMapper();
$tagMapper->setId($this->getFirstId());
$tag = $tagMapper->selectTag();
if (!is_null($tag->getId())) {
return parent::update($this->table, $tag_, $where);
} elseif (is_null($tag->getId())) {
throw new Exception('Tag does not exist !');
}
} catch (InvalidArgumentException $e) {
print $e->getMessage();
exit;
} catch (Exception $e) {
print $e->getMessage();
exit;
}
}
/**
*
* @param Message $message_
* @throws InvalidArgumentException
*/
public function updateMessage(Message $message_)
{
if (is_null($this->table)) {
throw new InvalidArgumentException('Attribute "table" can\'t be NULL !');
}
if (isset($this->id) && !is_null($this->id)) {
$where = 'id = ' . $this->id;
}
return parent::update($this->table, $message_, $where);
}
/**
*
* @param Incoming $incoming_
* @throws InvalidArgumentException
*/
public function updateIncoming(Incoming $incoming_)
{
try {
if (is_null($this->table)) {
throw new InvalidArgumentException('Attribute "table" can\'t be NULL !');
}
if (isset($this->id) && !is_null($this->id)) {
$where = 'id = ' . $this->id;
}
return parent::update($this->table, $incoming_, $where);
} catch (InvalidArgumentException $e) {
print $e->getMessage();
exit;
}
}
/**
*
* @param Comment $comment_
* @throws InvalidArgumentException
*/
public function updateComment(Comment $comment_)
{
try {
if (is_null($this->table)) {
throw new InvalidArgumentException('Attribute "table" can\'t be NULL !');
}
if (isset($this->id) && !is_null($this->id)) {
$where = 'id = ' . $this->id;
}
$comment = $this->selectComment();
if (!emptyObjectMethod($comment)) {
return parent::update($this->table, $comment_, $where);
} else {
throw new Exception('Comment doesn\'t exist !');
}
} catch (InvalidArgumentException $e) {
print $e->getMessage();
exit;
} catch (Exception $e) {
print $e->getMessage();
exit;
}
}
public static function AddStudy(&$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 testUpdate()
{
// get a patient by id
$patientObject = new Patient();
$patientObject->name = 'PLN2';
$patientObject->dob = '2002-01-01';
$patientObject->sex = 'F';
$patientObject->uid = 'PID2;';
$patientID = Mapper::add($patientObject);
// Modify one field
$patientObject->name = 'PLN3';
// Update database and get object
Mapper::update($patientObject, $patientID);
$patientResult = Mapper::getStatic('Patient', $patientID);
// compared object we just added with its "base" object
// we make sure id match
$patientObject->id = $patientID;
$this->assertTrue($patientResult['Patient'][0]->equals($patientObject) == True);
// update "silly" object to create one object which alread exists
$existingID = Mapper::update($patientObject, -1);
// should return the id of the object which already exists
$this->assertTrue($patientID == $existingID);
//update object that does not exist
$patientObject->name = 'PLN4';
$existingID = Mapper::update($patientObject, -1);
// update should return 0 if object does not exist
$this->assertTrue($existingID == 0);
// clean the DB
Mapper::delete('Patient', $patientID);
}
$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], $feedResult['Feed'][0]->id);
exit(0);
// delete the temp file
unlink($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);
}
}
