/**
* Constructs a new Debug-Object.
*
* The first parameter has to be the file name with extension, but without directory. The second
* parameter has to be a valid and existing directory path with trainling directory separator
* (make sure the directory is writable). Standard value for this paramteer is null. If the
* directory is null or invalid "data/logs/" will be used. If the specified file doesn't exist
* it will created. If it is not possible to create a file a NonFatalException will be thrown.
*
* @param string File for saving the logdata
* @param string Valid Directory for saving the logfile or null (directory will be "data/logs/")
* @throws NonFatalException
*/
public function __construct($file, $dir = null) {
if ($dir === null || is_dir($dir) === false) {
$dir = 'data/logs/';
}
$this->file = new File($dir.basename($file));
if ($this->file->create() === false) {
throw new NonFatalException('Could not create log file "'.$this->file->relPath().'".');
}
if ($this->file->readable() === false || $this->file->writable() === false) {
$this->file->setPermissions(666);
}
$this->logs = array();
$this->benchmarks = array();
$this->temp = array();
}
public function fetch($key)
{
$cacheFile = CacheStorageFile::getCacheFile($key);
if (File::exists($cacheFile) && File::readable($cacheFile)) {
return @file_get_contents($cacheFile);
}
return false;
}
/**
* Constructs a new Debug-Object.
*
* The first parameter has to be the file name with extension, but without directory.
* Standard value is null, then the filename will be "internal.log".
* The second parameter has to be a valid and existing directory with trailing slash.
* Standard value is also null, then the directory will be "data/logs/" (make sure that it is writable).
* If the specified file doesn't exist, it will created.
* If it is not possible to create a file nn Exception will be thrown.
*
* @param string File for saving the logdata or null (filename is internal.log then)
* @param string Directory for saving the logfile or null (directory is data/logs/ then)
* @throws Exception
*/
public function __construct($file = null, $dir = null)
{
if ($dir == null || is_dir($dir) == false) {
$dir = 'data/logs/';
}
if ($file == null) {
$file = 'internal.log';
}
$this->file = new File($dir . basename($file));
if ($this->file->create() == false) {
throw new Exception('Could not create log file in method Debug::__construct().');
}
if ($this->file->readable() == false || $this->file->writable() == false) {
$writable = new CHMOD(666);
$this->file->setChmod($writable);
}
$this->logs = array();
$this->benchmarks = array();
$this->temp = array();
}
private function loadContainers($containers)
{
if (!File::exists($containers)) {
throw new Exception("Invalid container path");
}
foreach (glob("{$containers}/*.js") as $file) {
if (!File::readable($file)) {
throw new Exception("Could not read container config: {$file}");
}
if (is_dir($file)) {
// support recursive loading of sub directories
$this->loadContainers($file);
} else {
$this->loadFromFile($file);
}
}
}
public function open($dir, $filename, $write = false)
{
$this->_currentFile = null;
$this->_currentFileLastModified = null;
$ds = $this->getDataSource();
$file = new File($filepath = $ds->config['path'] . DS . $dir . DS . $filename, false);
if (!$file) {
return false;
}
if (!$file->readable()) {
return false;
}
if ($write && !$file->writable()) {
return false;
}
$this->_currentFile = $file;
$this->_currentFileLastChange = $file->lastChange();
return $file;
}
/**
* beforeRender callback function
*
* @param Controller $controller
* @return array contents for panel
*/
public function beforeRender(Controller $controller)
{
$data = array();
$dir = new Folder(LOGS);
$files = $dir->find();
foreach ($files as $log) {
$file = new File(LOGS . $log);
$name = $file->name();
$data[$name] = array();
if (!$file->readable()) {
$data[$name]['content'] = __('This log file is unreadable.');
continue;
}
$data[$name]['lastChange'] = date('Y-m-d H:i:s', $file->lastChange());
if ($file->size() > $this->readBytes) {
$file->offset(-$this->readBytes, SEEK_END);
}
$data[$name]['content'] = $file->read($this->readBytes);
}
return $data;
}
/**
* @param keyFile The file containing your private key for signing requests.
*/
public function __construct($keyFile = null)
{
$this->keyName = 'http://' . $_SERVER["HTTP_HOST"] . Config::get('web_prefix') . '/public.cer';
if (!empty($keyFile)) {
$rsa_private_key = false;
$privateKey = null;
try {
if (File::exists($keyFile)) {
if (File::readable($keyFile)) {
$rsa_private_key = @file_get_contents($keyFile);
} else {
throw new Exception("Could not read keyfile ({$keyFile}), check the file name and permission");
}
}
if (!$rsa_private_key) {
$rsa_private_key = '';
} else {
$phrase = Config::get('private_key_phrase') != '' ? Config::get('private_key_phrase') : null;
if (strpos($rsa_private_key, "-----BEGIN") === false) {
$privateKey .= "-----BEGIN PRIVATE KEY-----\n";
$chunks = str_split($rsa_private_key, 64);
foreach ($chunks as $chunk) {
$privateKey .= $chunk . "\n";
}
$privateKey .= "-----END PRIVATE KEY-----";
} else {
$privateKey = $rsa_private_key;
}
if (!($rsa_private_key = @openssl_pkey_get_private($privateKey, $phrase))) {
throw new Exception("Could not create the key");
}
}
} catch (Exception $e) {
throw new Exception("Error loading private key: " . $e);
}
$this->privateKey = $rsa_private_key;
}
}
/**
* Tests a file's contents against magic items
*
* @param string $file Absolute path to a file
* @param array $items
* @return mixed A string containing the MIME type of the file or false if no pattern matched
* @access private
*/
function __test($file, $items)
{
$File = new File($file);
if (!$File->readable()) {
return false;
}
$File->open('rb');
foreach ($items as $item) {
if ($result = $this->__testRecursive($File, $item)) {
return $result;
}
}
return false;
}
/**
* Handles existent but not readable files
*
* @access protected
* @return mixed
*/
function _handleNotReadable()
{
if (!$this->__File->readable() && $this->__File->exists()) {
$message = 'File `' . $this->shortPath($this->__File->pwd()) . '`';
$message .= ' exists but is not readable.';
$this->out($message);
return true;
}
return false;
}
/**
* Setup for display or download the given file.
*
* If $_SERVER['HTTP_RANGE'] is set a slice of the file will be
* returned instead of the entire file.
*
* ### Options keys
*
* - name: Alternate download name
* - download: If `true` sets download header and forces file to be downloaded rather than displayed in browser
*
* @param string $path Path to file. If the path is not an absolute path that resolves
* to a file, `APP` will be prepended to the path.
* @param array $options Options See above.
* @return void
* @throws NotFoundException
*/
public function file($path, $options = array())
{
$options += array('name' => null, 'download' => null);
if (strpos($path, '../') !== false || strpos($path, '..\\') !== false) {
throw new NotFoundException(__d('cake_dev', 'The requested file contains `..` and will not be read.'));
}
if (!is_file($path)) {
$path = APP . $path;
}
$file = new File($path);
if (!$file->exists() || !$file->readable()) {
if (Configure::read('debug')) {
throw new NotFoundException(__d('cake_dev', 'The requested file %s was not found or not readable', $path));
}
throw new NotFoundException(__d('cake', 'The requested file was not found'));
}
$extension = strtolower($file->ext());
$download = $options['download'];
if ((!$extension || $this->type($extension) === false) && $download === null) {
$download = true;
}
$fileSize = $file->size();
if ($download) {
$agent = env('HTTP_USER_AGENT');
if (preg_match('%Opera(/| )([0-9].[0-9]{1,2})%', $agent)) {
$contentType = 'application/octet-stream';
} elseif (preg_match('/MSIE ([0-9].[0-9]{1,2})/', $agent)) {
$contentType = 'application/force-download';
}
if (!empty($contentType)) {
$this->type($contentType);
}
if ($options['name'] === null) {
$name = $file->name;
} else {
$name = $options['name'];
}
$this->download($name);
$this->header('Content-Transfer-Encoding', 'binary');
}
$this->header('Accept-Ranges', 'bytes');
$httpRange = env('HTTP_RANGE');
if (isset($httpRange)) {
$this->_fileRange($file, $httpRange);
} else {
$this->header('Content-Length', $fileSize);
}
$this->_clearBuffer();
$this->_file = $file;
}
public function grabFiles()
{
$validItems = $this->getFileRules();
App::uses('Folder', 'Utility');
App::uses('File', 'Utility');
$result = array();
foreach ($validItems as $k => &$item) {
$dir = new Folder($item['path']);
$files = $dir->find($item['regex'], true);
foreach ($files as $file) {
$f = new File($item['path'] . DS . $file);
$validItems[$k]['files'][] = array('filename' => $file, 'filesize' => $f->size(), 'read' => $f->readable(), 'write' => $f->writable(), 'execute' => $f->executable());
}
}
return $validItems;
}
/**
* undocumented function
*
* @return void
*/
function parent()
{
$config = $this->config();
if ($config['id'] == 1 || empty($config['fork'])) {
return array();
}
if (!empty($config['fork'])) {
$path = Configure::read("Content.{$config['repo']['type']}") . 'repo' . DS . $config['url'] . '.git' . DS;
}
$File = new File($path . 'permissions.ini');
if (!$File->readable()) {
if (!$File->create()) {
return false;
}
}
return $File->read();
}
/**
* Retrieve (cached) metadata of a file
*
* @param Model $Model
* @param string $file An absolute path to a file
* @param integer $level level of amount of info to add, `0` disable, `1` for basic, `2` for detailed info
* @return mixed Array with results or false if file is not readable
*/
function metadata(&$Model, $file, $level = 1)
{
if ($level < 1) {
return array();
}
extract($this->settings[$Model->alias]);
$File = new File($file);
if (!$File->readable()) {
return false;
}
$checksum = $File->md5(true);
if (isset($this->__cached[$Model->alias][$checksum])) {
$data = $this->__cached[$Model->alias][$checksum];
}
if ($level > 0 && !isset($data[1])) {
$data[1] = array('size' => $File->size(), 'mime_type' => MimeType::guessType($File->pwd()), 'checksum' => $checksum);
}
if ($level > 1 && !isset($data[2])) {
$Media = Media::factory($File->pwd());
if ($Media->name === 'Audio') {
$data[2] = array('artist' => $Media->artist(), 'album' => $Media->album(), 'title' => $Media->title(), 'track' => $Media->track(), 'year' => $Media->year(), 'length' => $Media->duration(), 'quality' => $Media->quality(), 'sampling_rate' => $Media->samplingRate(), 'bit_rate' => $Media->bitRate());
} elseif ($Media->name === 'Image') {
$data[2] = array('width' => $Media->width(), 'height' => $Media->height(), 'ratio' => $Media->ratio(), 'quality' => $Media->quality(), 'megapixel' => $Media->megapixel());
} elseif ($Media->name === 'Text') {
$data[2] = array('characters' => $Media->characters(), 'syllables' => $Media->syllables(), 'sentences' => $Media->sentences(), 'words' => $Media->words(), 'flesch_score' => $Media->fleschScore(), 'lexical_density' => $Media->lexicalDensity());
} elseif ($Media->name === 'Video') {
$data[2] = array('title' => $Media->title(), 'year' => $Media->year(), 'length' => $Media->duration(), 'width' => $Media->width(), 'height' => $Media->height(), 'ratio' => $Media->ratio(), 'quality' => $Media->quality(), 'bit_rate' => $Media->bitRate());
} else {
$data[2] = array();
}
}
for ($i = $level, $result = array(); $i > 0; $i--) {
$result = array_merge($result, $data[$i]);
}
$this->__cached[$Model->alias][$checksum] = $data;
return Set::filter($result);
}
function __loadDbItems()
{
// variable used to determine the read dir time
$acdate = strtotime("now");
// check to see whether a valid directory was passed to the script
if ($this->Session->read('User.dirname_get')) {
// if it is valid, we'll set it as the directory to read data from
$this->dirpath = $this->Session->read('User.dirname_get');
} else {
// if it is invalid, we'll use the default directory
$this->dirpath = Configure::read('default_get_dir');
}
// use Folder class
$dir = new Folder($this->dirpath);
// try to change the current working directory to the one from wich i want to read contents from
if (!$dir->cd($this->dirpath)) {
// if the change failed, I'll use the default directory
$this->dirpath = Configure::read('default_get_dir');
$dir->cd(Configure::read('default_get_dir'));
}
// once the current working directory is set, it is opened and read from
$dir_listing = $dir->read(true, false, true);
if ($dir_listing) {
// while there are still entries
foreach ($dir_listing[1] as $entry) {
// if the entry is to be shown (not part of the 'not_to_be_shown' array)
if (!in_array($entry, Configure::read('not_to_be_shown'))) {
$file = new File($entry);
if ($file->readable()) {
// store the file extension
$fext = $file->ext();
// store the filename
$fname = $file->name;
// store the lowercased extension
$lfext = strtolower($fext);
// store size of file into KB
$fsize = round($file->size() / 1024, 2);
// store date of file
$fidate = $file->lastChange();
// store dirpath with file
$finfokey = $entry;
// store absfilename
$fnameabs = $file->name();
// define check for filestatus_status (if updated)
$update_status = Configure::read('msg_items_file_unselected');
// check table fileinfo for update or insert
$file_info = $this->FileInfo->find('first', array('conditions' => array('fileinfo_id' => $finfokey), 'fields' => array('fileinfo_id', 'fileinfo_filedate')));
if (!empty($file_info)) {
$this->FileInfo->read(null, $file_info['FileInfo']['fileinfo_id']);
$this->FileInfo->set(array('fileinfo_dirname' => $this->dirpath, 'fileinfo_filename' => $fname, 'fileinfo_absfilename' => $fnameabs, 'fileinfo_ext' => $lfext, 'fileinfo_size' => $fsize, 'fileinfo_filedate' => $fidate, 'fileinfo_timenow' => $acdate));
$this->FileInfo->save();
// check data modified file is changed
if ($fidate > $file_info['FileInfo']['fileinfo_filedate']) {
$update_status = Configure::read('msg_items_file_updated');
}
} else {
$this->FileInfo->create();
$this->FileInfo->set(array('fileinfo_id' => $finfokey, 'fileinfo_dirname' => $this->dirpath, 'fileinfo_filename' => $fname, 'fileinfo_absfilename' => $fnameabs, 'fileinfo_ext' => $lfext, 'fileinfo_size' => $fsize, 'fileinfo_filedate' => $fidate, 'fileinfo_timenow' => $acdate));
$this->FileInfo->save();
}
// check table filestatus for update or insert
$file_status = $this->FileStatus->find('first', array('conditions' => array('filestatus_fileinfo_key' => $finfokey, 'filestatus_users_id' => $this->Session->read('User.id')), 'fields' => array('filestatus_id', 'filestatus_status')));
if (!empty($file_status)) {
if ($file_status['FileStatus']['filestatus_status'] == Configure::read('msg_items_file_selected') && $update_status != Configure::read('msg_items_file_updated')) {
$update_status = Configure::read('msg_items_file_selected');
}
$this->FileStatus->read(null, $file_status['FileStatus']['filestatus_id']);
$this->FileStatus->set(array('filestatus_status' => $update_status, 'filestatus_users_id' => $this->Session->read('User.id'), 'filestatus_timenow' => $acdate));
$this->FileStatus->save();
} else {
$this->FileStatus->create();
$this->FileStatus->set(array('filestatus_fileinfo_key' => $finfokey, 'filestatus_status' => $update_status, 'filestatus_users_id' => $this->Session->read('User.id'), 'filestatus_timenow' => $acdate));
$this->FileStatus->save();
}
}
}
}
// check consistency : delete from db files that's removed from directory
$file_info_del = $this->FileInfo->deleteAll(array('fileinfo_timenow < ' => $acdate));
if (!$file_info_del) {
$this->log('DownloadsController:__loadDbItems - Unable delete FileInfo model record', Configure::read('log_file'));
}
// check consistency : delete from db files that's removed from directory
$file_status_del = $this->FileStatus->deleteAll(array('filestatus_timenow < ' => $acdate, 'filestatus_users_id' => $this->Session->read('User.id')));
if (!$file_status_del) {
$this->log('DownloadsController:__loadDbItems - Unable delete FileStatus model record', Configure::read('log_file'));
}
}
}
public function get($key, $expiration = false)
{
if (!$expiration) {
// if no expiration time was given, fall back on the global config
$expiration = Config::get('cache_time');
}
$cacheFile = $this->getCacheFile($key);
// See if this cache file is locked, if so we wait upto 5 seconds for the lock owning process to
// complete it's work. If the lock is not released within that time frame, it's cleaned up.
// This should give us a fair amount of 'Cache Stampeding' protection
if ($this->isLocked($cacheFile)) {
$this->waitForLock($cacheFile);
}
if (File::exists($cacheFile) && File::readable($cacheFile)) {
$now = time();
if (($mtime = @filemtime($cacheFile)) !== false && $now - $mtime < $expiration) {
if (($data = @file_get_contents($cacheFile)) !== false) {
$data = unserialize($data);
return $data;
}
}
}
return false;
}
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'));
}
}
}
/**
* Retrieve (cached) metadata of a file
*
* @param Model $Model
* @param string $file An absolute path to a file
* @param integer $level level of amount of info to add, `0` disable, `1` for basic, `2` for detailed info
* @return mixed Array with results or false if file is not readable
*/
function metadata(&$Model, $file, $level = 1)
{
if ($level < 1) {
return array();
}
extract($this->settings[$Model->alias]);
$File = new File($file);
if (!$File->readable()) {
return false;
}
$checksum = $File->md5(true);
if (isset($this->__cached[$Model->alias][$checksum])) {
$data = $this->__cached[$Model->alias][$checksum];
}
if ($level > 0 && !isset($data[1])) {
$data[1] = array('size' => $File->size(), 'mime_type' => Mime_Type::guessType($File->pwd()), 'checksum' => $checksum);
}
if ($level > 1 && !isset($data[2])) {
$data[2] = array();
try {
$Info = Media_Info::factory(array('source' => $File->pwd()));
foreach ($Info->all() as $key => $value) {
$data[2][Inflector::underscore($key)] = $value;
}
} catch (Exception $E) {
}
}
for ($i = $level, $result = array(); $i > 0; $i--) {
$result = array_merge($result, $data[$i]);
}
$this->__cached[$Model->alias][$checksum] = $data;
return $result;
}
function importAnnotationsAndDocuments()
{
$this->Round = $this->Project->Round;
$this->Document = $this->Project->Document;
$this->UsersRound = $this->Project->User->UsersRound;
$this->AnnotatedDocument = $this->Round->AnnotatedDocument;
$this->Type = $this->Project->Type;
$this->Annotation = $this->Type->Annotation;
$maxAnnotation = $this->Annotation->find('first', array('recursive' => -1, 'fields' => 'id', 'order' => 'id DESC'));
if (isset($maxAnnotation['Annotation']['id'])) {
$maxAnnotation = $maxAnnotation['Annotation']['id'];
} else {
$maxAnnotation = 0;
}
$maxType = $this->Project->Type->find('first', array('recursive' => -1, 'fields' => 'id', 'order' => 'id DESC'));
if (isset($maxType['Type']['id'])) {
$maxType = $maxType['Type']['id'];
} else {
$maxType = 0;
}
if ($this->request->is('post') || $this->request->is('put')) {
$maxAnnotation++;
App::uses('Folder', 'Utility');
App::uses('File', 'Utility');
App::uses('CakeTime', 'Utility');
$scriptTimeLimit = Configure::read('scriptTimeLimit');
set_time_limit($scriptTimeLimit);
$users = $this->request->data['User']['User'];
//App::import('Vendor', 'htmLawed', array('file' => 'htmLawed' . DS . 'htmLawed.php'));
$zipFile = new File($this->request->data['Project']['File']['tmp_name'], false, 0777);
$projectName = ucwords(pathinfo($this->request->data['Project']['File']['name'], PATHINFO_FILENAME));
if ($zipFile->exists() && !empty($users)) {
$filesAllowed = Configure::read('filesAllowed');
$zip = new ZipArchive();
if (!$zip->open($zipFile->pwd(), ZipArchive::CREATE)) {
$zipFile->remove();
throw new Exception("Failed to open Zip archive\n");
}
$path = Configure::read('uploadFolder');
$path = $path . uniqid();
//creamos la carpeta de descarga para el usuario si no existe
$extractFolder = new Folder($path, true, 0700);
$zip->extractTo($extractFolder->pwd());
$zip->close();
$zipFile->delete();
// I am deleting this file
$rounds = array();
$db = $this->Project->getDataSource();
$db->query("ALTER TABLE annotations AUTO_INCREMENT = {$maxAnnotation}");
$db->execute("LOCK TABLES " . $this->Annotation->table . " " . $this->Type->table . " WRITE");
$db->begin();
$db->useNestedTransactions = false;
$this->Project->create();
if ($this->Project->save(array('Project' => array("title" => $projectName, "description" => ""), "User" => array('User' => $users)))) {
//creamos round de anotacion automatica
$this->Round->create();
if (!$this->Round->save(array('Round' => array("title" => "Round for job " . date("Y/m/d"), "project_id" => $this->Project->id, "description" => "-", 'ends_in_date' => date("Y-m-d", strtotime("+30 day")), 'trim_helper' => true, 'whole_word_helper' => true, 'punctuation_helper' => true, 'start_document' => 0, 'end_document' => 0, 'is_visible' => 0)))) {
$extractFolder->delete();
$db->rollback();
$db->execute("UNLOCK TABLES");
throw new Exception("Round work can not be saved");
}
array_push($rounds, $this->Round->id);
foreach ($users as $user) {
foreach ($rounds as $round) {
$this->UsersRound->create();
if (!$this->UsersRound->save(array('state' => 0, 'round_id' => $round, 'user_id' => $user))) {
$extractFolder->delete();
$db->rollback();
$db->execute("UNLOCK TABLES");
throw new Exception("This UsersRound can not be save:" . $fileName);
}
}
}
$typesText = new File($extractFolder->pwd() . DS . 'types.txt', false, 0644);
if (!$typesText->exists()) {
$extractFolder->delete();
$db->rollback();
$db->execute("UNLOCK TABLES");
throw new Exception("types.txt not exist in zip file");
}
$count = new File($extractFolder->pwd() . DS . 'count.txt', false, 0644);
if (!$count->exists()) {
$extractFolder->delete();
$db->rollback();
$db->execute("UNLOCK TABLES");
throw new Exception("count.txt not exist in zip filer");
}
$typesText = $typesText->read();
$count = $count->read();
$count = intval($count) + 1;
//buscamos la anotacion final con dicho Id si ya existe no se puede crear el proyecto
$existLastId = $this->Annotation->find('count', array('recursive' => -1, 'conditions' => array('id' => $count)));
$existInitialId = $this->Annotation->find('count', array('recursive' => -1, 'conditions' => array('id' => $count - ($count - $maxAnnotation))));
if ($existInitialId > 0) {
$extractFolder->delete();
$db->rollback();
$db->execute("UNLOCK TABLES");
throw new Exception("the first id already exist in Marky");
}
if ($existLastId > 0) {
$extractFolder->delete();
$db->rollback();
$db->execute("UNLOCK TABLES");
throw new Exception("the last id already exist in Marky");
}
$types = preg_split("/[\r\n]+/", trim($typesText));
$typesMap = array();
$defaultColors = Configure::read('defaultColors');
$colorCont = 0;
foreach ($types as $type) {
//debug($types);
$type = explode("\t", $type);
if (sizeof($type) > 1) {
$typeName = $type[0];
$typeId = $type[1];
$typeName = str_replace(' ', '_', $typeName);
if (!empty($defaultColors[$colorCont])) {
$color = $defaultColors[$colorCont];
$colorCont++;
} else {
$color = array(rand(50, 255), rand(50, 255), rand(50, 255));
}
$this->Type->create();
if ($this->Type->save(array('Type' => array('id' => $typeId, 'name' => $typeName, 'project_id' => $this->Project->id, 'colour' => $color[0] . ',' . $color[1] . ',' . $color[2] . ',1'), 'Round' => array('Round' => $rounds)))) {
$typesMap[$typeName] = $this->Type->id;
} else {
$extractFolder->delete();
$db->rollback();
$db->execute("UNLOCK TABLES");
// debug($types);
// debug($this->Project->Type->validationErrors);
throw new Exception("This type can not be save" . $type);
}
} else {
$extractFolder->delete();
$db->rollback();
$db->execute("UNLOCK TABLES");
// debug($types);
// debug($this->Project->Type->validationErrors);
throw new Exception("This type can not be save" . $type);
}
}
$files = $extractFolder->find('.*.html', true);
if (empty($files)) {
$extractFolder->delete();
$db->rollback();
$db->execute("UNLOCK TABLES");
throw new Exception("The html documents can not be read");
}
//$config = array('cdata' => 1, 'safe' => 1, 'keep_bad' => 6, 'no_depreca ted_attr' => 2, 'valid_xhtml' => 1, 'abs_url' => 1);
$annotationsAcumulate = array();
foreach ($files as $file) {
//sleep(5);
$fileName = substr($file, 0, strrpos($file, '.'));
$file = new File($extractFolder->pwd() . DS . $file);
if ($file->readable()) {
//$content = '<p>' . preg_replace("/\.\s*\n/", '.</p><p>', $file->read()) . '</p>';
$content = $file->read();
if (strlen($content) > 1) {
$file->close();
$date = date("Y-m-d H:i:s");
$document = $this->Document->find('first', array('recursive' => -1, 'conditions' => array('external_id' => $fileName)));
if (empty($document)) {
$this->Document->create();
if (!$this->Document->save(array('Document' => array('external_id' => $fileName, 'title' => $fileName, 'html' => strip_tags($content), 'created' => $date), 'Project' => array('Project' => $this->Project->id)))) {
$extractFolder->delete();
$db->rollback();
$db->execute("UNLOCK TABLES");
throw new Exception("This Document can not be save:" . $fileName);
}
} else {
$this->Document->id = $document['Document']['id'];
if (!$this->Document->save(array('Document' => array('id' => $this->Document->id), 'Project' => array('Project' => $this->Project->id)))) {
$extractFolder->delete();
$db->rollback();
$db->execute("UNLOCK TABLES");
throw new Exception("This Document - Project can not be save");
}
}
$annotations = $this->getAnnotations($content, $typesMap, $this->Document->id);
$tam = count($annotations);
$modes = Configure::read('annotationsModes');
// $results = gzdeflate($content, 9);
foreach ($users as $user) {
foreach ($rounds as $round) {
$this->AnnotatedDocument->create();
if (!$this->AnnotatedDocument->save(array('text_marked' => $content, 'document_id' => $this->Document->id, 'mode' => $modes["AUTOMATIC"], 'round_id' => $round, 'user_id' => $user))) {
$extractFolder->delete();
$db->rollback();
$db->execute("UNLOCK TABLES");
throw new Exception("This UsersRound can not be save:" . $fileName);
}
if (!empty($annotations)) {
for ($index = 0; $index < $tam; $index++) {
$annotations[$index]['user_id'] = $user;
$annotations[$index]['round_id'] = $round;
//// if ($round == $this->Round->id) {
////// $annotations[$index]['id'] = $maxAnnotation;
////// $maxAnnotation++;
//// }
}
$annotationsAcumulate = array_merge($annotationsAcumulate, $annotations);
}
}
}
if (count($annotationsAcumulate) > 500) {
if (!$this->Project->Type->Annotation->saveMany($annotationsAcumulate)) {
//debug($annotations);
debug($this->Project->Type->Annotation->validationErrors[0]);
debug($fileName);
$extractFolder->delete();
$db->rollback();
$db->execute("UNLOCK TABLES");
throw new Exception("Annotations can not be save");
}
$annotationsAcumulate = array();
}
}
}
}
if (count($annotationsAcumulate) > 0) {
if (!$this->Annotation->saveMany($annotationsAcumulate)) {
//debug($annotations);
debug($this->Project->Type->Annotation->validationErrors[0]);
debug($fileName);
$extractFolder->delete();
$db->rollback();
$db->execute("UNLOCK TABLES");
throw new Exception("Annotations can not be save");
}
}
// throw new Exception;
$extractFolder->delete();
$db->commit();
$db->execute("UNLOCK TABLES");
$this->Session->setFlash(__('Project has been created with documents imported'), 'success');
$this->redirect(array('action' => 'index'));
}
$extractFolder->delete();
} else {
$this->Session->setFlash(__('Choose almost one user and one file'));
}
}
$userConditions = array('group_id' => 2);
$users = $this->Project->User->find('list', array('conditions' => $userConditions));
$this->set(compact('users', 'maxAnnotation', 'maxType'));
}
/**
* uploadFile method
* Esta funcion es la encargada de gestionar los ficheros del
* usurio.
* En projectos add gestiona (crear,eliminar)
* En projectos edit gestiona (crear) dado que los ficheros se eliminan de la BD
* La direccion de la carpeta del usuario se establece con la variable
* Configure::read('uploadFilesPath') y el mail del usuario (e mail es unico)
* @require App::uses('Folder', 'Utility');
* @require App::uses('File', 'Utility');
* @require UploadHandler.php
* @throws exception
* @return void
*/
public function uploadFile($projectId = null)
{
App::import('Vendor', 'uploader', array('file' => 'jQuery-File-Upload' . DS . 'UploadHandler.php'));
App::uses('Folder', 'Utility');
App::uses('File', 'Utility');
$uploadPath = Configure::read('uploadFilesPath');
$filesAllowed = Configure::read('filesAllowed');
$maxUploads = Configure::read('max_upload_files');
$maxFileSize = $this->filesize2bytes(Configure::read('max_file_size'));
if ($maxUploads == 0) {
$maxUploads = 99999;
}
$path = $uploadPath;
//para que no moleste con los permisos
//ini_set("display_errors", 0);
//error_reporting(0);
$this->autoRender = false;
$email = $this->Auth->user('email');
//si no esta logueado
if (!$this->Auth->loggedIn()) {
print "One joker!!";
exit;
} else {
$folder = new Folder();
//si se puede crear la carpeta
if ($folder->create($path)) {
//chmod($path, 0600);
// $path = $path . DS . $email;
$path = $path . DS . tempnam(sys_get_temp_dir(), '');
if ($folder->create($path)) {
//si no existe la carpeta se crea
$folder = new Folder($path, true, 0700);
//chmod($path, 0600);
$absolutePath = $folder->path . DS;
$options = array('script_url' => Router::url(array('controller' => 'ProjectResources', 'action' => 'uploadFile')), 'upload_dir' => $absolutePath, 'upload_url' => $this->webroot . $path . DS, 'user_dirs' => false, 'mkdir_mode' => 0700, 'param_name' => 'files', 'delete_type' => 'DELETE', 'access_control_allow_origin' => '*', 'access_control_allow_credentials' => false, 'access_control_allow_methods' => array('OPTIONS', 'HEAD', 'GET', 'POST', 'PUT', 'PATCH', 'DELETE'), 'access_control_allow_headers' => array('Content-Type', 'Content-Range', 'Content-Disposition'), 'download_via_php' => false, 'accept_file_types' => '/(\\.|\\/)' . $filesAllowed . '$/i', 'max_file_size' => $maxFileSize, 'min_file_size' => 1, 'max_number_of_files' => $maxUploads, 'max_width' => null, 'max_height' => null, 'min_width' => 1, 'min_height' => 1, 'discard_aborted_uploads' => true, 'orient_image' => false);
$upload_handler = new UploadHandler($options, false);
switch ($_SERVER['REQUEST_METHOD']) {
case 'HEAD':
case 'GET':
throw new Exception();
$upload_handler->get();
break;
case 'POST':
case 'PUT':
$group_id = $this->Session->read('group_id');
if ($group_id == 1) {
$this->ProjectResource->Project->id = $projectId;
if (!$this->ProjectResource->Project->exists()) {
throw new NotFoundException(__('Invalid project '));
}
$response = $upload_handler->post();
$packagedFiles = array();
$files = $folder->find('.*.' . $filesAllowed);
if (!empty($files)) {
foreach ($files as $file) {
$file = new File($folder->pwd() . DS . $file, 644);
if ($file->readable()) {
// $md5 = $file->md5();
$name = $file->name();
$ext = $file->ext();
$content = $file->read();
$fileSize = $file->size();
$file->close();
$data = array('name' => $name, 'file' => $content, 'extension' => $ext, 'project_id' => $projectId, 'size' => $fileSize);
$this->ProjectResource->create();
if ($this->ProjectResource->save($data)) {
$packagedFiles[$name . "." . $ext] = $this->ProjectResource->id;
}
}
}
if (!empty($packagedFiles)) {
$files = $response['files'];
$size = sizeof($files);
for ($index = 0; $index < $size; $index++) {
$file = $files[$index];
if (isset($packagedFiles[$file->name])) {
$file->url = Router::url(array('controller' => 'ProjectResources', 'action' => 'downloadFile', $packagedFiles[$file->name], $projectId));
$file->deleteUrl = Router::url(array('controller' => 'ProjectResources', 'action' => 'deleteFile', $packagedFiles[$file->name], $projectId));
} else {
$file->error = "Could not be saved";
}
}
return $this->correctResponseJson($response);
// $this->correctResponseJson(array("error" => "Could not be saved"));
}
}
if (!$folder->delete()) {
throw new Exception("Error deleting files");
}
return $this->correctResponseJson($response);
}
break;
case 'DELETE':
break;
default:
// header('HTTP/1.0 405 Method Not Allowed');
}
exit;
}
} else {
throw new Exception();
}
}
}
private static function loadFile($fileName)
{
// this hack prevents loadFile from trying to load .jar resources
if (empty($fileName) || strpos($fileName, 'res://') !== false) {
return '';
}
if (Config::get('debug')) {
if (!File::exists($fileName)) {
throw new Exception("JsLibrary file missing: {$fileName}");
}
if (!is_file($fileName)) {
throw new Exception("JsLibrary file is not a file: {$fileName}");
}
if (!File::readable($fileName)) {
throw new Exception("JsLibrary file not readable: {$fileName}");
}
}
if (!($content = @file_get_contents($fileName))) {
throw new Exception("JsLibrary error reading file: {$fileName}");
}
return $content;
}
/**
* Returns the average server load in the last minute.
*
* Note: This is currently not available on windows.
*
* @return Load average of the last minute
*/
public static function getLoad() {
$serverload = -1;
// Not implemented on Windows
if(self::getOS() == self::WINDOWS) {
return $serverload;
}
if (function_exists('sys_getloadavg')) {
list($serverload) = sys_getloadavg();
}
$proc = new File('/proc/loadavg');
if($serverload == -1 && $proc->exists() && $proc->readable()) {
$load = $proc->read(File::READ_STRING, File::BINARY);
if ($load !== false) {
list($serverload) = explode(b" ", $load);
$serverload = trim($serverload);
}
}
if ($serverload == -1 && function_exists('exec')) {
$load = @exec("uptime");
if(preg_match("~load averages?:\s?([\d\.]+)~i", $load, $serverload)) {
list(,$serverload) = $serverload;
}
}
if (empty($serverload)) {
$serverload = -1;
}
return $serverload;
}
/**
* Setup for display or download the given file
*
* @param string $path Path to file
* @param array $options Options
* ### Options keys
* - name: Alternate download name
* - download: If `true` sets download header and forces file to be downloaded rather than displayed in browser
* @return void
* @throws NotFoundException
*/
public function file($path, $options = array())
{
$options += array('name' => null, 'download' => null);
if (!is_file($path)) {
$path = APP . $path;
}
$file = new File($path);
if (!$file->exists() || !$file->readable()) {
if (Configure::read('debug')) {
throw new NotFoundException(__d('cake_dev', 'The requested file %s was not found or not readable', $path));
}
throw new NotFoundException(__d('cake', 'The requested file was not found'));
}
$extension = strtolower($file->ext());
$download = $options['download'];
if ((!$extension || $this->type($extension) === false) && is_null($download)) {
$download = true;
}
$fileSize = $file->size();
if ($download) {
$agent = env('HTTP_USER_AGENT');
if (preg_match('%Opera(/| )([0-9].[0-9]{1,2})%', $agent)) {
$contentType = 'application/octetstream';
} elseif (preg_match('/MSIE ([0-9].[0-9]{1,2})/', $agent)) {
$contentType = 'application/force-download';
}
if (!empty($contentType)) {
$this->type($contentType);
}
if (is_null($options['name'])) {
$name = $file->name;
} else {
$name = $options['name'];
}
$this->download($name);
$this->header('Accept-Ranges', 'bytes');
$httpRange = env('HTTP_RANGE');
if (isset($httpRange)) {
list(, $range) = explode('=', $httpRange);
$size = $fileSize - 1;
$length = $fileSize - $range;
$this->header(array('Content-Length' => $length, 'Content-Range' => 'bytes ' . $range . $size . '/' . $fileSize));
$this->statusCode(206);
$file->open('rb', true);
$file->offset($range);
} else {
$this->header('Content-Length', $fileSize);
}
} else {
$this->header('Content-Length', $fileSize);
}
$this->_clearBuffer();
$this->_file = $file;
}
/**
* Handles existent but not readable files
*
* @access protected
* @return mixed
*/
function _handleNotReadable()
{
if (!$this->__File->readable() && $this->__File->exists()) {
$this->out('File exists but is not readable');
return true;
}
}
/**
* testReadable method
*
* @return void
*/
public function testReadable()
{
$someFile = new File(TMP . 'some_file.txt', false);
$this->assertTrue($someFile->open());
$this->assertTrue($someFile->readable());
$someFile->close();
$someFile->delete();
}
public function importTsv()
{
App::uses('Folder', 'Utility');
App::uses('File', 'Utility');
if ($this->request->is('post') || $this->request->is('put')) {
if (isset($this->request->data['Document']['File']) && $this->request->data['Document']['File']['size'] > 0) {
$fileName = $this->request->data['Document']['File']['name'];
$extension = pathinfo($fileName, PATHINFO_EXTENSION);
$checkextension = array("tsv", "txt");
if (in_array($extension, $checkextension)) {
//your code goes here.
$db = $this->Document->getDataSource();
$timeLimit = Configure::read('scriptTimeLimit');
set_time_limit($timeLimit);
$db->begin();
$project_id = $this->request->data['Project']['Project'];
$file = new File($this->request->data['Document']['File']['tmp_name']);
if ($file->readable()) {
$content = $file->read();
$file->close();
$lines = explode("\n", $content);
if (!empty($lines)) {
$size = count($lines);
for ($index = 0; $index < $size; $index++) {
if (strlen($lines[$index]) > 1) {
$section = explode("\t", $lines[$index]);
if (sizeof($section) == 3) {
$external_id = strtoupper($section[0]);
$title = $section[1];
$corpus = $section[2];
$html = "<div class='corpusSections'><h3 class='title'>" . $title . "</h3><div class='abstract'>" . $corpus . "</div></div>";
$data = array('title' => $title, 'external_id' => $external_id, 'html' => $html);
if ($project_id != 0) {
$data = array('Project' => array('id' => $project_id), 'Document' => $data);
}
$conditions = array('external_id' => $external_id);
if (!$this->Document->hasAny($conditions)) {
$this->Document->create();
if (!$this->Document->save($data)) {
$db->rollback();
$index++;
throw new Exception("Line " . $index . " could not be save");
}
} else {
$this->Document->DocumentsProject->create();
$document = $this->Document->find('first', array('recursive' => -1, 'fields' => 'id', 'conditions' => $conditions));
$document_id = $document['Document']['id'];
$data = array('project_id' => $project_id, 'document_id' => $document_id);
if (!$this->Document->DocumentsProject->save($data)) {
$db->rollback();
$index++;
throw new Exception("Line " . $index . " could not be save");
}
}
} else {
$db->rollback();
$index++;
throw new Exception("Line " . $index . " is incorrect");
}
}
}
$this->Session->setFlash(__('All documents have been saved'), 'success');
$db->commit();
if ($project_id != 0) {
$this->redirect(array('controller' => 'projects', 'action' => 'view', $project_id));
} else {
$this->redirect(array('controller' => 'documents', 'action' => 'index'));
}
}
}
}
}
$this->Session->setFlash(__('The document could not be processed. Incorrect format or file empty (try txt or tsv file).'));
}
$projects = $this->Document->Project->find('list');
$this->set(compact('projects'));
}
