/**
* Returns true if given datetime string is within this week.
*
* @param int|string|DateTime $dateString UNIX timestamp, strtotime() valid string or DateTime object
* @param string|DateTimeZone $timezone User's timezone string or DateTimeZone object
*
* @return bool True if datetime string is within current week
* @see CakeTime::isThisWeek()
* @link http://book.cakephp.org/2.0/en/core-libraries/helpers/time.html#testing-time
*/
public function isThisWeek($dateString, $timezone = NULL)
{
return $this->_engine->isThisWeek($dateString, $timezone);
}
public function analysis()
{
$this->Cookie = $this->Components->load('Cookie');
$this->Cookie->type('rijndael');
$projects = array();
// $this->Cookie->time = '999 hours';
if ($this->request->is(array('post', 'put'))) {
// debug($this->request->data);
if (isset($this->request->data['Participant']['email'])) {
$email = $this->request->data['Participant']['email'];
}
if (isset($this->request->data['Participant']['code'])) {
$code = $this->request->data['Participant']['code'];
}
$project_id = -1;
if (isset($this->request->data['Project']['Project'])) {
$project_id = $this->request->data['Project']['Project'];
}
if ($this->data['Participant']['remember_me'] && isset($code) && isset($email)) {
$cookie = array();
$cookie['email'] = $email;
$cookie['code'] = $code;
if (isset($project_id)) {
$cookie['project_id'] = $project_id;
}
$this->Cookie->write('participantData', $cookie, true, '+2 weeks');
} else {
if ($this->Cookie->check('participantData')) {
$this->Cookie->destroy('participantData');
}
}
$projects = $this->getParticipantProjects($email, $code);
App::uses('Folder', 'Utility');
App::uses('File', 'Utility');
if (isset($this->request->data['Participant']['analyze_File']) && $this->request->data['Participant']['analyze_File']['size'] > 0 && !empty($projects)) {
/* ============================================= */
/* ==============Load analysis=================== */
/* ============================================= */
if ($this->request->data['Participant']['analyze_File']['size'] > $this->filesize2bytes(Configure::read('max_file_size'))) {
$this->Session->setFlash("The file can not be more than " . Configure::read('max_file_size'));
return $this->redirect(array('controller' => 'Participants', 'action' => 'analysis'));
}
$file = $this->request->data['Participant']['analyze_File']['name'];
if (pathinfo($file, PATHINFO_EXTENSION) != 'tsv') {
$this->Session->setFlash("The file must be in TSV format");
return $this->redirect(array('controller' => 'Participants', 'action' => 'analysis'));
}
$file = new File($this->request->data['Participant']['analyze_File']['tmp_name']);
if ($file->readable()) {
$content = $file->read();
$file->close();
$lines = explode("\n", $content);
$incorrectFormat = empty($lines);
$count = 0;
$size = count($lines);
for ($index = 0; $index < $size; $index++) {
if (strlen(trim($lines[$index])) > 0) {
if (!$incorrectFormat) {
$columns = explode("\t", $lines[$index]);
for ($i = 0; $i < count($columns); $i++) {
if (strlen(trim($columns[$i])) == 0) {
$incorrectFormat = true;
}
}
$incorrectFormat = $incorrectFormat || sizeof($columns) != 5;
$count++;
} else {
break;
}
}
}
// $correctFormat = $this->correctTsvFormat($file, 5);
if ($incorrectFormat) {
// $count=$this->incorrecLineTsvFormat($file);
$this->Session->setFlash("Incorrect content file. Line {$count} is incorrect. " . "Content file must be in this format WO2009026621A1->A:12:24->1->0.99->paliperidone");
return $this->redirect(array('controller' => 'Participants', 'action' => 'analysis'));
}
$participantID = $this->Participant->find('first', array("recursive" => -1, "fields" => array("id"), "conditions" => array('Participant.email' => $email, 'Participant.code' => $code)));
$participantID = $participantID["Participant"]["id"];
$this->request->data['Participant']['id'] = $participantID;
$this->participantSaveConnection($this->request->data['Participant'], "uploadAnalysis");
// $this->Participant->UploadedAnnotation->deleteAll(array(
// "participant_id" => $participantID));
//
// $this->Participant->PredictionDocument->deleteAll(array(
// "participant_id" => $participantID,
// "project_id" => $project_id
// ));
$javaJarPath = Configure::read('javaJarPath');
$analyze_program = Configure::read('analyze_program');
$runJava = Configure::read('runJava');
$program = $javaJarPath . DS . $analyze_program;
$path = $this->request->data['Participant']['analyze_File']['tmp_name'];
$file = new File($path);
if ($file->readable()) {
$newPath = $file->Folder->path . DS . md5(date('Y-m-d H:i:s:u')) . $file->name() . "mtmp";
$file->copy($newPath);
$path = $newPath;
} else {
throw new Exception("Ops! file could not be readed");
}
$arguments = "{$project_id}\t{$participantID}\t{$email}\t{$path}";
// exec("nohup java -jar $program $arguments", $output);
$javaLog = ".." . DS . 'java_jars' . DS . "java.log";
$date = date('Y-m-d H:i:s');
exec("echo \"{$date}:{$runJava} {$program} {$arguments}\" >> {$javaLog} 2>&1 &");
exec("{$runJava} {$program} {$arguments} >> {$javaLog} 2>&1 &");
$this->Session->setFlash("Your predictions are being processed, we will send you an email when the analysis finish", 'success');
return $this->redirect(array('controller' => 'Participants', 'action' => 'analysis'));
}
} else {
if (isset($this->request->data['Participant']['results_File']['size']) && $this->request->data['Participant']['results_File']['size'] > 0) {
if ($this->request->data['Participant']['results_File']['size'] > $this->filesize2bytes(Configure::read('max_file_size'))) {
$this->Session->setFlash("The file can not be more than " . Configure::read('max_file_size'));
return $this->redirect(array('controller' => 'Participants', 'action' => 'analysis'));
}
/* ============================================= */
/* =====================Results================= */
/* ============================================= */
$file = new File($this->request->data['Participant']['results_File']['tmp_name']);
if ($file->readable()) {
$content = $file->read();
$file->close();
$content = $this->decrypt($content);
$results = json_decode(trim($content), true);
// debug($results);
if (!empty($results)) {
$projects = $this->getParticipantProjects($email, $code, $results['project_id']);
if (!empty($projects)) {
$goldenSet = $this->Participant->GoldenProject->find('first', array('recursive' => -1, 'fields' => array('user_id', 'round_id'), 'conditions' => array('project_id' => $results['project_id'])));
if (!empty($goldenSet)) {
$isModified = !$this->Participant->PredictionFile->hasAny(array('participant_id' => $results['Participant']['id'], 'modified' => $results['date']));
$results['Participant']['isModified'] = $isModified;
$results['Golden']['user_id'] = $goldenSet['GoldenProject']['user_id'];
$results['Golden']['round_id'] = $goldenSet['GoldenProject']['round_id'];
$this->Session->write("analysisResults", $results);
$this->redirect(array('action' => 'results'));
} else {
$this->Session->setFlash("This golden set have been deleted");
}
} else {
$this->Session->setFlash("This file does not correspond to your credentials");
}
} else {
$this->Session->setFlash("This file is corrupted");
}
} else {
$this->Session->setFlash("This file is corrupted");
}
} else {
if (empty($projects)) {
$this->Session->setFlash("You are not in any project");
} else {
$this->Session->setFlash("One team prediction file or one result file is needed");
}
}
}
} else {
$cookie = $this->Cookie->read('participantData');
if (isset($cookie)) {
if (isset($cookie['email']) && $cookie['code']) {
$this->request->data['Participant']['email'] = $cookie['email'];
$this->request->data['Participant']['code'] = $cookie['code'];
$this->request->data['Participant']['remember_me'] = true;
if (isset($cookie['project_id'])) {
$this->request->data['Project']['Project'] = $cookie['project_id'];
}
$projects = $this->getParticipantProjects($cookie['email'], $cookie['code']);
if (empty($projects)) {
$this->Cookie->destroy('participantData');
}
} else {
$this->Cookie->destroy('participantData');
}
}
$this->loadModel('Post');
$this->Post->recursive = -1;
$this->Post->contain(false, array('User' => array('username', 'surname', 'full_name', 'image', 'image_type', 'id')));
$this->Post->paginate = array('limit' => 5, 'order' => array('modified' => 'DESC'));
$this->set("posts", $this->paginate($this->Post));
}
$this->set('projects', $projects);
App::uses('CakeTime', 'Utility');
$finalDate = Configure::read('final_date_to_upload_tasks');
$startDate = Configure::read('initial_date_to_upload_tasks');
$isEnd = CakeTime::isPast($finalDate);
$isFuture = CakeTime::isFuture($startDate);
$isThisWeek = CakeTime::isThisWeek($finalDate);
$isToday = CakeTime::isTomorrow(CakeTime::fromString($finalDate));
$finalDate = CakeTime::format($finalDate, "%B %e, %Y");
$startDate = CakeTime::format($startDate, "%B %e, %Y");
$this->set('isEnd', $isEnd);
$this->set('isFuture', $isFuture);
$this->set('isThisWeek', $isThisWeek);
$this->set('isToday', $isToday);
$this->set('finalDate', $finalDate);
$this->set('startDate', $startDate);
//// $key = "xVO5JLSLOTpKX4YRyFpJXNYb1STQK26mHAzgNK6bwS697XzK8ZE5kEA8R7gajaI9fE6HfemeLhg28nqbGTmh5Dv5uKydSOoM4BHlQ43mvH4h0Jl3xFDcv95fRnY9wYAluS1WFi9QOLc2JDUOsN3ggNzypHuZcPaAjBklfsNH98qkX5brqEnfMUubPOUCtpTEUmtvVNq2oTGKSArEuSuuKRnMHtlbKvl4XbaAUvSfajF4DtHwLa2qaWU6pNXLHf16";
//// $key = "FFF3454D1E9CCDE00101010101010101";
// $value = "63612bb6b56ef964bc2a6add5e0697deadde735fd4ca966d7b762f61b2b4cb14a14500";
//// $value = base64_decode($value);
//// debug($value);
//// $result = Security::rijndael($value, $key, 'decrypt');
// $result = $this->decrypt($value);
//// $resultE = Security::rijndael($value, $key, 'encrypt');
// $this->set(compact('result', 'resultE'));
}
