/**
* Calculates the current age of someone born on $birthdate.
* Source: stackoverflow.com/questions/3776682/php-calculate-age
* @param sing $birthdate The birthdate.
* @return integer The calculated age.
* @access public
* @static
*/
public static function ageFromBirthdate($birthdate)
{
// convert to format: YYYY-MM-DD
$clean_birthdate = date('Y-m-d', CakeTime::fromString($birthdate));
if (CakeTime::isFuture($clean_birthdate)) {
throw new OutOfRangeException("Birthdate is in the future: {$clean_birthdate}", BedrockTime::EXCEPTION_CODE_FUTURE_BIRTHDATE);
}
//explode the date to get month, day and year
$parts = explode('-', $clean_birthdate);
//get age from date or birthdate
$age = intval(date('md', date('U', mktime(0, 0, 0, $parts[1], $parts[2], $parts[0]))) > date('md') ? date('Y') - $parts[0] - 1 : date('Y') - $parts[0]);
return $age;
}
/**
* Days in theme
* @param int $theme_id
*/
public function days($theme_id = null, $user_id = null)
{
if (!$theme_id) {
return;
}
$options = array('recursive' => -1, 'conditions' => array('Day.theme_id' => $theme_id), 'order' => array('data ASC'));
$rows = $this->Day->find('all', $options);
foreach ($rows as $key => $row) {
$row['Day']['isFuture'] = false;
$row['Day']['isPast'] = false;
$row['Day']['isToday'] = false;
$row['Day']['comments'] = $this->Comment->find('count', array('conditions' => array('Comment.user_id' => !$this->isUser() ? $user_id : $this->getUserId(), 'Comment.day_id' => $row['Day']['id'])));
if (CakeTime::isFuture($row['Day']['data'])) {
$row['Day']['isFuture'] = true;
}
if (CakeTime::isPast($row['Day']['data'])) {
$row['Day']['isPast'] = true;
}
if (CakeTime::isToday($row['Day']['data'])) {
$row['Day']['isToday'] = true;
}
$data[] = $row['Day'];
}
$this->set($data);
$this->set('_serialize', array_keys($data));
}
public function oldCopyRound($projectId = null)
{
if ($this->request->is('post') || $this->request->is('put')) {
//$this -> autoRender = false;
if (!empty($this->request->data['Round']['Round'])) {
$oldRoundId = $this->request->data['Round']['Round'];
$round = $this->Round->find('first', array('recursive' => -1, 'conditions' => array('Round.id' => $oldRoundId)));
if (trim($this->request->data['Round']['title']) == '' || !isset($this->request->data['Round']['title'])) {
$this->Session->setFlash('Please select one Title');
$this->redirect(array('controller' => 'rounds', 'action' => 'copyRound', $projectId));
}
App::uses('CakeTime', 'Utility');
if (CakeTime::isFuture($round['Round']['ends_in_date'])) {
$this->Round->id = $round['Round']['id'];
$date = CakeTime::format('-1 days', '%Y-%m-%d');
$this->Round->saveField('ends_in_date', $date);
}
if (empty($this->request->data['Round']['User'])) {
$this->Session->setFlash('You must choose at least one user');
$this->redirect(array('controller' => 'rounds', 'action' => 'copyRound', $projectId));
} else {
$oldRoundId = $this->request->data['Round']['Round'];
$this->Round->create();
$this->request->data['Round']['ends_in_date'] = NULL;
$users = $this->request->data['Round']['User'];
$conditions_userRounds = array('UsersRound.round_id' => $oldRoundId, 'UsersRound.user_id' => $users);
//guardamos los usuarios en condiciones
unset($this->request->data['Round']['User']);
$title = $this->request->data['Round']['title'];
$this->request->data['Round']['title'] = $title . '-[0%]';
$errors = "";
//$db = $this->Round->getDataSource();
//$db->begin();
if ($this->Round->save($this->request->data, false)) {
//se deshabilita el save para poder guardar rounds con ends_in_date = NULL
//esta bandera marcara que un round esta en estado de copia
$this->Session->setFlash('We are creating a new version of the round. Please be patient', 'information');
//cortamos la ejecucion parab el usuario pero el script sigue en ejecucion
//de esta forma el usuario puedeseguir navegando
$this->backGround(array('controller' => 'projects', 'action' => 'view', $round['Round']['project_id']));
$round_id = $this->Round->id;
$newRoundId = $this->Round->id;
$size_userRounds = $this->Round->UsersRound->find('count', array('recursive' => -1, 'conditions' => $conditions_userRounds));
/**
* tamaño de particiones
* Haremos una particion de los rounds para no sobrecargar la memoria
* ** */
if ($size_userRounds > 0) {
//hacemos partioces de user_rounds de 100
$particiones_userRounds = 100;
$size_userRounds_total = $size_userRounds;
//si el tamaño es mayor que la particion calculamos cuantas veces vamos a tener que hacer
if ($size_userRounds > $particiones_userRounds) {
$fin_userRounds = $size_userRounds / $particiones_userRounds;
//calculamos el numero de beces a la baja
// por ejemplo 2.5 se haces dos veces
$fin_userRounds = floor($fin_userRounds);
//si existe resto se hace una vez mas
if ($size_userRounds % $particiones_userRounds != 0) {
$fin_userRounds++;
}
} else {
// si no la particion es = al tamaño
$particiones_userRounds = $size_userRounds;
$fin_userRounds = 1;
}
$contador_userRounds = 0;
$procces_userRounds = 0;
$time = date('Y-m-d H:i:s');
//variables para monotorizar la copia
$worked = 0;
$procces = 0;
while ($contador_userRounds < $fin_userRounds) {
$usersRounds = $this->Round->UsersRound->find('all', array('offset' => $procces_userRounds, 'limit' => $particiones_userRounds, 'recursive' => -1, 'fields' => array('UsersRound.id', 'UsersRound.user_id', 'UsersRound.document_id', 'UsersRound.text_marked'), 'conditions' => $conditions_userRounds));
//se eligen bucles for en vez de bucles foreach dado que son mas rapidos si se van a modificar datos
//http://www.phpbench.com/
$usersRoundTam = sizeof($usersRounds);
for ($i = 0; $i < $usersRoundTam; $i++) {
$procces++;
$worked = $procces / $size_userRounds_total * 100;
if (round($worked) % 10 == 0) {
$data = array('Round' => array('title' => $title . '-[' . round($worked) . '%]'));
$this->Round->save($data);
}
$usersRounds[$i]['UsersRound']['created'] = $time;
$conditions = array('Annotation.round_id' => $oldRoundId, 'Annotation.document_id' => $usersRounds[$i]['UsersRound']['document_id'], 'Annotation.user_id' => $usersRounds[$i]['UsersRound']['user_id'], 'Annotation.users_round_id' => $usersRounds[$i]['UsersRound']['id']);
$textoForMatches = $usersRounds[$i]['UsersRound']['text_marked'];
$usersRounds[$i]['UsersRound']['round_id'] = $newRoundId;
unset($usersRounds[$i]['UsersRound']['id']);
unset($usersRounds[$i]['UsersRound']['text_marked']);
$this->Round->UsersRound->create();
if ($this->Round->UsersRound->save($usersRounds[$i])) {
$size_annotations = $this->Round->UsersRound->Annotation->find('count', array('recursive' => -1, 'conditions' => $conditions));
if ($size_annotations > 0) {
$parseKey = Configure::read('parseKey');
$parseIdAttr = Configure::read('parseIdAttr');
/**
* Particiones de anotaciones
*/
$particiones_annotations = 400;
if ($size_annotations > $particiones_annotations) {
$fin_annotations = $size_annotations / $particiones_annotations;
$fin_annotations = floor($fin_annotations);
if ($size_annotations % $particiones_annotations != 0) {
$fin_annotations++;
}
} else {
$particiones_annotations = $size_annotations;
$fin_annotations = 1;
}
$contador_annotations = 0;
$procces_annotations = 0;
$annotations_id = array();
while ($contador_annotations < $fin_annotations) {
$annotations = $this->Round->UsersRound->Annotation->find('all', array('offset' => $procces_annotations, 'limit' => $particiones_annotations, 'recursive' => -1, 'conditions' => $conditions));
$annotationTam = sizeof($annotations);
for ($j = 0; $j < $annotationTam; $j++) {
$oldId = $annotations[$j]['Annotation']['id'];
unset($annotations[$j]['Annotation']['id']);
//insertamos nuevo user round
$annotations[$j]['Annotation']['users_round_id'] = $this->Round->UsersRound->id;
//insertamos nuevo round
$annotations[$j]['Annotation']['round_id'] = $newRoundId;
if (empty($annotations[$j]['Annotation']['annotated_text'])) {
$annotations[$j]['Annotation']['annotated_text'] = 'empty?';
}
$this->Round->UsersRound->Annotation->create();
if ($this->Round->UsersRound->Annotation->save($annotations[$j])) {
$newId = $this->Round->UsersRound->Annotation->id;
array_push($annotations_id, $newId);
$this->Round->UsersRound->Annotation->query("insert into annotations_questions ( annotation_id,question_id,answer)\n SELECT " . $newId . ",question_id,answer FROM annotations_questions where annotation_id = {$oldId}");
}
}
//$i = 0; $i < $annotationTam; $i++
if ($procces_annotations + $particiones_annotations * 2 > $size_annotations) {
$procces_annotations += $particiones_annotations;
$particiones_annotations = $size_annotations - $procces_annotations;
} else {
$procces_annotations += $particiones_annotations;
}
$contador_annotations++;
}
/*
* A partir de este punto machearemos las anotaciones en el documento actualizando su ID
* */
preg_match_all("/<mark[^>]*" . $parseKey . "[^>]*[^>]*>/", $textoForMatches, $matches);
$numberOfMaches = sizeof($matches[0]);
// el sistema es flexible frente a contratiempos imprevistos como que el umero de anotaciones parseadas sean distintos a la base de datos
$pos = -1;
$k = 0;
$ultimoId = -1;
while ($k < $numberOfMaches) {
preg_match('/[^>]*' . $parseIdAttr . '=.?(\\d+).?[^>]/', $matches[0][$k], $id);
if ($ultimoId != $id) {
$ultimoId = $id;
$pos++;
}
// debug($annotations_id[$pos]);
$search = $matches[0][$k];
// if(!isset($annotations_id[$pos])) {
// debug($id);
// }
$replace = preg_replace('/' . $parseIdAttr . '=.(\\d+)./', $parseIdAttr . '="' . $annotations_id[$pos] . '"', $search);
$textoForMatches = str_replace($search, $replace, $textoForMatches);
$k++;
}
if ($pos + 1 != sizeof($annotations_id)) {
// debug(sizeof($annotations_id));
// debug($numberOfMaches);
// debug($pos);
// debug($usersRounds[$i]['UsersRound']['document_id']);
$errors = "This round is courrupted. Unexpected error has occurred. Do not worry this is not a fatal error. But please contact the administrator. Error: 'other number annotations database VS parse'";
}
}
//guardamos el documento con el texto anotado actualizado
$usersRounds[$i]['UsersRound']['text_marked'] = $textoForMatches;
unset($usersRounds[$i]['UsersRound']['id']);
$this->Round->UsersRound->save($usersRounds[$i]);
}
//$this->Round->UsersRound->save($usersRounds[$i])
}
//$i = 0; $i < $usersRoundTam; $i++
if ($procces_userRounds + $particiones_userRounds * 2 >= $size_userRounds) {
$procces_userRounds += $particiones_userRounds;
$particiones_userRounds = $size_userRounds - $procces_userRounds;
} else {
$procces_userRounds += $particiones_userRounds;
}
$contador_userRounds++;
}
}
//finalmente actualizamos los datos del round con los datos que metio el usuario e introducimos los tipos de anotacion
//del round origen
$date = CakeTime::format('+30 days', '%Y-%m-%d');
$data = array('Round' => array('description' => $errors, 'ends_in_date' => $date, 'title' => $title), 'User' => array('User' => $users));
if ($this->Round->save($data)) {
//$this->Round->commit();
$round_id = $this->Round->id;
$this->Round->query("insert into types_rounds ( round_id,type_id) select {$round_id},type_id\n from types_rounds \n where round_id = {$oldRoundId}");
//$db->commit();
//$db->close();
} else {
//$db->rollback();
//$db->close();
}
} else {
//$db->rollback();
//$db->close();
$this->Session->setFlash('Unexpected error ocurs, error Id: roundCopySave');
$this->redirect(array('controller' => 'rounds', 'action' => 'copyRound', $projectId));
}
}
} else {
$this->Session->setFlash('There are no data to be copied!');
$this->redirect(array('controller' => 'rounds', 'action' => 'copyRound', $projectId));
}
} else {
$this->Round->Project->id = $projectId;
if (!$this->Round->Project->exists()) {
throw new NotFoundException(__('Invalid round'));
}
//!$this->Round->exists()
$deleteCascade = Configure::read('deleteCascade');
$conditions = array('project_id' => $projectId, 'ends_in_date IS NOT NULL');
if ($deleteCascade) {
$conditions = array('project_id' => $projectId, 'ends_in_date IS NOT NULL', 'title!=\'Removing...\'');
}
$rounds = $this->Round->find('list', array('conditions' => $conditions));
if (empty($rounds)) {
$this->Session->setFlash('Insufficient data for this operation');
$this->redirect(array('controller' => 'projects', 'action' => 'view', $projectId));
} else {
$cond = array('project_id' => $projectId);
$users = $this->Round->Project->ProjectsUser->find('all', array('fields' => 'user_id', 'conditions' => $cond, 'recursive' => -1));
$users = $this->flatten($users);
$userConditions = array('id' => $users);
if ($deleteCascade) {
$userConditions = array('username !=' => 'Removing...', 'id' => $users);
}
$users = $this->Round->User->find('list', array('conditions' => $userConditions));
}
$this->set('rounds', $rounds);
$this->set('users', $users);
$this->set('projectId', $projectId);
}
}
function uploadFinalPredictions()
{
$this->Cookie = $this->Components->load('Cookie');
$this->Cookie->type('rijndael');
// $this->Cookie->time = '999 hours';
if ($this->request->is(array('post', 'put'))) {
// debug($this->request->data);
$email = $this->request->data['Participant']['email'];
$code = $this->request->data['Participant']['code'];
$task = $this->request->data['Participant']["task"];
$run = $this->request->data['Participant']["run"];
$maxUploadTask = Configure::read('max_participant_task_upload');
$tasks = Configure::read('biocreative_tasks');
$finalDate = Configure::read('final_date_to_upload_tasks');
$startDate = Configure::read('initial_date_to_upload_tasks');
if (!in_array($task, $tasks) && $run < 0 && $run > 5) {
$this->Session->setFlash("Incorrect data");
return $this->redirect(array('controller' => 'Participants', 'action' => 'analysis'));
}
App::uses('CakeTime', 'Utility');
$isEnd = CakeTime::isPast($finalDate);
$isFuture = CakeTime::isFuture($startDate);
if ($isEnd || $isFuture) {
$this->Session->setFlash("The final delivery date has expired");
return $this->redirect(array('controller' => 'Participants', 'action' => 'analysis'));
}
$project_id = -1;
if ($this->data['Participant']['remember_me'] && isset($code) && isset($email)) {
$cookie = array();
$cookie['email'] = $email;
$cookie['code'] = $code;
$this->Cookie->write('participantData', $cookie, true, '+2 weeks');
} else {
if ($this->Cookie->check('participantData')) {
$this->Cookie->destroy('participantData');
}
}
App::uses('Folder', 'Utility');
App::uses('File', 'Utility');
// debug($this->request->data);
if ($this->request->data['Participant']['final_prediction']['size'] > 0) {
/* ============================================= */
/* ==============Load analysis=================== */
/* ============================================= */
if ($this->request->data['Participant']['final_prediction']['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 = $this->request->data['Participant']['final_prediction']['name'];
if (pathinfo($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']['final_prediction']['tmp_name']);
if ($file->readable()) {
$content = $file->read();
$file->close();
$lines = explode("\n", $content);
$incorrectFormat = empty($lines);
$count = 0;
$size = count($lines);
$correctColumns = 5;
if ($task == "CPD") {
$correctColumns = 4;
}
for ($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) != $correctColumns;
$count++;
} else {
break;
}
}
}
// $correctFormat = $this->correctTsvFormat($file, 5);
if ($incorrectFormat) {
// $count=$this->incorrecLineTsvFormat($file);
if ($task == "CPD") {
$this->Session->setFlash("Incorrect content file. Line {$count} is incorrect. " . "Content file must be contain 4 columns");
} else {
$this->Session->setFlash("Incorrect content file. Line {$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'));
}
$participant = $this->Participant->find('first', array("recursive" => -1, "fields" => array("id", "team_id"), "conditions" => array('Participant.email' => $email, 'Participant.code' => $code)));
$participantID = $participant["Participant"]["id"];
$team_id = $participant["Participant"]["team_id"];
$this->request->data['Participant']['id'] = $participantID;
$this->participantSaveConnection($this->request->data['Participant'], "uploadTeamPrediction");
$path = Configure::read('participantsPath');
$path = $path . DS . $task . DS . $team_id;
$dir = new Folder($path, true, 0755);
$tempPath = $this->request->data['Participant']['final_prediction']['tmp_name'];
$file = new File($tempPath);
if ($file->readable()) {
$content = $file->read();
$newPath = $dir->pwd() . DS . "{$run}.tsv";
$file->copy($newPath);
$path = $newPath;
chmod($newPath, 0200);
$data = array('participant_id' => $participantID, 'biocreative_task' => $task, 'run' => $run);
$finalfile = $this->Participant->FinalPrediction->find('first', array("conditions" => $data, 'fields' => 'id'));
if (!empty($finalfile)) {
$this->Participant->FinalPrediction->id = $finalfile['FinalPrediction']['id'];
$this->Session->setFlash("The file has been updated successfully", "success");
$type = "updated";
} else {
$this->Participant->FinalPrediction->create();
$this->Session->setFlash("The file has been created successfully", "success");
$type = "uploaded";
}
$data = array('participant_id' => $participantID, 'run' => $run, 'email' => $email, 'biocreative_task' => $task, 'file' => $content, 'file_name' => $this->request->data['Participant']['final_prediction']['name']);
if (!$this->Participant->FinalPrediction->save($data)) {
$this->Session->setFlash("File could not be saved");
return $this->redirect(array('controller' => 'Participants', 'action' => 'analysis'));
} else {
$this->sendMailWithAttachment("finalPredictionSuccess", $email, "[MARKYT - BIOCREATIVE V (CHEMDNER)] Final submision", array("run" => $run, "type" => $type, "task" => $task), array("{$run}.tsv" => $tempPath));
}
return $this->redirect(array('controller' => 'Participants', 'action' => 'analysis'));
}
} else {
throw new Exception("Ops! file could not be readed");
}
} else {
$this->Session->setFlash("One team prediction file is needed");
return $this->redirect(array('controller' => 'Participants', 'action' => 'analysis'));
}
}
}
