/** Index action */
public function indexAction()
{
$this->requireAdminPrivileges();
$this->view->pageTitle = 'Cleanup Module Configuration';
$form = new Cleanup_Form_Admin();
if ($this->getRequest()->isPost()) {
$data = $this->getRequest()->getPost();
if ($form->isValid($data)) {
$values = $form->getValues();
foreach ($values as $key => $value) {
if ($key !== 'csrf' && !is_null($value)) {
$this->Setting->setConfig($key, $value, $this->moduleName);
}
}
$this->ModuleComponent->Admin->schedulePerformCleanupJob($values[CLEANUP_DAYS_TO_KEEP_PARTIAL_FILES_KEY], UtilityComponent::getTempDirectory(), $this->userSession->Dao);
}
$form->populate($data);
} else {
$elements = $form->getElements();
foreach ($elements as $element) {
$name = $element->getName();
if ($name !== 'csrf' && $name !== 'submit') {
$value = $this->Setting->getValueByName($name, $this->moduleName);
if (!is_null($value)) {
$form->setDefault($name, $value);
}
}
}
}
$this->view->form = $form;
session_start();
}
/**
* will create default paths in the temporary directory
* for any properties not already set, except for the
* condor bin dir; imposing a firmer hand on the user.
*
* @param array $currentConfig current configuration
* @return array
*/
protected function createDefaultConfig($currentConfig)
{
$defaultConfigDirs = array(MIDAS_BATCHMAKE_TMP_DIR_PROPERTY => MIDAS_BATCHMAKE_DEFAULT_TMP_DIR, MIDAS_BATCHMAKE_BIN_DIR_PROPERTY => MIDAS_BATCHMAKE_DEFAULT_BIN_DIR, MIDAS_BATCHMAKE_SCRIPT_DIR_PROPERTY => MIDAS_BATCHMAKE_DEFAULT_SCRIPT_DIR, MIDAS_BATCHMAKE_APP_DIR_PROPERTY => MIDAS_BATCHMAKE_DEFAULT_APP_DIR, MIDAS_BATCHMAKE_DATA_DIR_PROPERTY => MIDAS_BATCHMAKE_DEFAULT_DATA_DIR);
$returnedConfig = array();
foreach ($currentConfig as $configProp => $configDir) {
if ((!isset($configProp) || !isset($configDir) || empty($configDir)) && array_key_exists($configProp, $defaultConfigDirs)) {
$returnedConfig[$configProp] = UtilityComponent::getTempDirectory($defaultConfigDirs[$configProp]);
} else {
$returnedConfig[$configProp] = $configDir;
}
}
return $returnedConfig;
}
/**
* Read in the streamed uploaded file and write it to a temporary file.
* Returns the name of the temporary file.
*/
private function _readUploadedFile($prefix)
{
UtilityComponent::setTimeLimit(0);
$inputfile = 'php://input';
$tmpfile = tempnam(UtilityComponent::getTempDirectory('misc'), $prefix);
$in = fopen($inputfile, 'rb');
$out = fopen($tmpfile, 'wb');
$bufSize = 1024 * 1024;
$size = 0;
// read from input and write into file
while (connection_status() == CONNECTION_NORMAL && ($buf = fread($in, $bufSize))) {
$size += strlen($buf);
fwrite($out, $buf);
}
fclose($in);
fclose($out);
return $tmpfile;
}
/**
* Upload a file to the server. PUT or POST is required.
* Will add the file as a bitstream to the item that was specified when
* generating the upload token in a new revision to that item, unless
* <b>revision</b> param is set.
*
* @path /system/upload
* @http POST
* @param uploadtoken The upload token (see <b>midas.upload.generatetoken</b>).
* @param filename The name of the bitstream that will be added to the item.
* @param length The length in bytes of the file being uploaded.
* @param mode (Optional) Stream or multipart. Default is stream.
* @param revision (Optional)
* If set, will add a new file into the existing passed in revision number.
* If set to "head", will add a new file into the most recent revision,
* and will create a new revision in this case if none exists.
* @param changes (Optional)
* The changes field on the affected item revision,
* e.g. for recording what has changed since the previous revision.
* @param license (Optional) The license for the revision.
* @return The item information of the item created or changed.
*
* @param array $args parameters
* @throws Exception
*/
public function uploadPerform($args)
{
/** @var ApihelperComponent $apihelperComponent */
$apihelperComponent = MidasLoader::loadComponent('Apihelper');
$apihelperComponent->validateParams($args, array('uploadtoken', 'filename', 'length'));
$request = Zend_Controller_Front::getInstance()->getRequest();
if (!$request->isPost() && !$request->isPut()) {
throw new Exception('POST or PUT method required', MIDAS_HTTP_ERROR);
}
list($userid, $itemid) = explode('/', $args['uploadtoken']);
/** @var ItemModel $itemModel */
$itemModel = MidasLoader::loadModel('Item');
/** @var UserModel $userModel */
$userModel = MidasLoader::loadModel('User');
$userDao = $userModel->load($userid);
if (!$userDao) {
throw new Exception('Invalid user id from upload token', MIDAS_INVALID_PARAMETER);
}
$item = $itemModel->load($itemid);
if ($item == false) {
throw new Exception('Unable to find item', MIDAS_INVALID_PARAMETER);
}
if (!$itemModel->policyCheck($item, $userDao, MIDAS_POLICY_WRITE)) {
throw new Exception('Permission error', MIDAS_INVALID_POLICY);
}
if (array_key_exists('revision', $args)) {
if (strtolower($args['revision']) == 'head') {
$revision = $itemModel->getLastRevision($item);
// if no revision exists, it will be created later
} else {
$revision = $itemModel->getRevision($item, $args['revision']);
if ($revision == false) {
throw new Exception('Unable to find revision', MIDAS_INVALID_PARAMETER);
}
}
}
$mode = array_key_exists('mode', $args) ? $args['mode'] : 'stream';
/** @var HttpuploadComponent $httpUploadComponent */
$httpUploadComponent = MidasLoader::loadComponent('Httpupload');
$apiSetup = $apihelperComponent->getApiSetup();
$httpUploadComponent->setTestingMode(Zend_Registry::get('configGlobal')->environment === 'testing');
if (array_key_exists('testingmode', $args)) {
$httpUploadComponent->setTestingMode(true);
if (!array_key_exists('localinput', $args)) {
$args['localinput'] = UtilityComponent::getTempDirectory() . '/' . $args['filename'];
}
}
// Use the Httpupload component to handle the actual file upload
if ($mode == 'stream') {
$result = $httpUploadComponent->process($args);
$filename = $result['filename'];
$filePath = $result['path'];
$fileSize = (int) $result['size'];
$fileChecksum = $result['md5'];
} elseif ($mode == 'multipart') {
if (!array_key_exists('file', $args) || !array_key_exists('file', $_FILES)) {
throw new Exception('Parameter file is not defined', MIDAS_INVALID_PARAMETER);
}
$file = $_FILES['file'];
$filename = $file['name'];
$filePath = $file['tmp_name'];
$fileSize = (int) $file['size'];
$fileChecksum = '';
} else {
throw new Exception('Invalid upload mode', MIDAS_INVALID_PARAMETER);
}
// get the parent folder of this item and notify the callback
// this is made more difficult by the fact the items can have many parents,
// just use the first in the list.
$parentFolders = $item->getFolders();
if (!isset($parentFolders) || !$parentFolders || count($parentFolders) === 0) {
// this shouldn't happen with any self-respecting item
throw new Exception('Item does not have a parent folder', MIDAS_INVALID_PARAMETER);
}
$firstParent = $parentFolders[0];
$validations = Zend_Registry::get('notifier')->callback('CALLBACK_CORE_VALIDATE_UPLOAD', array('filename' => $filename, 'size' => $fileSize, 'path' => $filePath, 'folderId' => $firstParent->getFolderId()));
foreach ($validations as $validation) {
if (!$validation['status']) {
unlink($filePath);
throw new Exception($validation['message'], MIDAS_INVALID_POLICY);
}
}
$license = array_key_exists('license', $args) ? $args['license'] : null;
$changes = array_key_exists('changes', $args) ? $args['changes'] : '';
$revisionNumber = null;
if (isset($revision) && $revision !== false) {
$revisionNumber = $revision->getRevision();
}
/** @var UploadComponent $uploadComponent */
$uploadComponent = MidasLoader::loadComponent('Upload');
$item = $uploadComponent->createNewRevision($userDao, $filename, $filePath, $changes, $item->getKey(), $revisionNumber, $license, $fileChecksum, false, $fileSize);
if (!$item) {
throw new Exception('Upload failed', MIDAS_INTERNAL_ERROR);
}
return $item->toArray();
}
/**
* The client sends the results to Midas Server (put request).
*
* @param token
*
* @param array $args parameters
* @throws Exception
*/
public function resultsserver($args)
{
$testingmode = false;
if (isset($_GET['testingmode']) && $_GET['testingmode'] == 1) {
$testingmode = true;
}
if (!$testingmode && $_SERVER['REQUEST_METHOD'] != 'POST') {
throw new Exception('Should be a put request.', MIDAS_INVALID_PARAMETER);
}
$authComponent = MidasLoader::loadComponent('Authentication');
$userDao = $authComponent->getUser($args, Zend_Registry::get('userSession')->Dao);
if ($userDao == false) {
throw new Exception('Unable to authenticate as a server. Please check credentials.', MIDAS_INVALID_PARAMETER);
}
/** @var GroupModel $groupModel */
$groupModel = MidasLoader::loadModel('Group');
$groupServer = $groupModel->load(MIDAS_GROUP_SERVER_KEY);
$users = $groupServer->getUsers();
$isServer = false;
foreach ($users as $user) {
if ($user->getKey() == $userDao->getKey()) {
$isServer = true;
}
}
if ($isServer == false) {
throw new Exception('Unable to authenticate as a server. Please check credentials.', MIDAS_INVALID_PARAMETER);
}
if (!file_exists(UtilityComponent::getTempDirectory() . '/remoteprocessing')) {
mkdir(UtilityComponent::getTempDirectory() . '/remoteprocessing');
}
/** @var RandomComponent $randomComponent */
$randomComponent = MidasLoader::loadComponent('Random');
$destination = UtilityComponent::getTempDirectory() . '/remoteprocessing/' . $randomComponent->generateInt();
while (file_exists($destination)) {
$destination = UtilityComponent::getTempDirectory() . '/remoteprocessing/' . $randomComponent->generateInt();
}
mkdir($destination);
if (!$testingmode) {
move_uploaded_file($_FILES['file']['tmp_name'], $destination . '/results.zip');
}
if ($testingmode) {
return array();
}
if (file_exists($destination . '/results.zip')) {
mkdir($destination . '/content');
$target_directory = $destination . '/content';
$filter = new Zend_Filter_Decompress(array('adapter' => 'Zip', 'options' => array('target' => $target_directory)));
$compressed = $filter->filter($destination . '/results.zip');
if ($compressed && file_exists($target_directory . '/parameters.txt')) {
$info = file_get_contents($target_directory . '/parameters.txt');
$info = JsonComponent::decode($info);
$job_id = $info['job_id'];
/** @var Remoteprocessing_JobModel $jobModel */
$jobModel = MidasLoader::loadModel('Job', 'remoteprocessing');
$jobDao = $jobModel->load($job_id);
$jobDao->setStatus(MIDAS_REMOTEPROCESSING_STATUS_DONE);
$jobModel->save($jobDao);
$info['pathResults'] = $destination . '/content';
$info['log'] = file_get_contents($target_directory . '/log.txt');
$info['userKey'] = $userDao->getKey();
Zend_Registry::get('notifier')->callback($info['resultCallback'], $info);
} else {
throw new Exception('Error, unable to unzip results.', MIDAS_INVALID_PARAMETER);
}
} else {
throw new Exception('Error, unable to find results.', MIDAS_INVALID_PARAMETER);
}
$this->_rrmdir($destination);
return array();
}
/**
* Return a temporary directory.
*
* @param string $subDirectory
* @param bool $createDirectory
* @return string
*/
protected function getTempDirectory($subDirectory = 'misc', $createDirectory = true)
{
return UtilityComponent::getTempDirectory($subDirectory, $createDirectory);
}
/**
* Get the temporary directory.
*
* @return string
*/
protected function getTempDirectory()
{
return UtilityComponent::getTempDirectory();
}
/**
* Google Cloud Storage upload callback.
*
* @param array $args
* @return array
* @throws Exception
*/
public function callback($args)
{
/** @var ApihelperComponent $apihelperComponent */
$apihelperComponent = MidasLoader::loadComponent('Apihelper');
$apihelperComponent->validateParams($args, array('uploadtoken'));
if (!Zend_Controller_Front::getInstance()->getRequest()->isPost()) {
throw new Exception('POST method required', MIDAS_HTTP_ERROR);
}
$uploadToken = $args['uploadtoken'];
$path = UtilityComponent::getTempDirectory() . '/' . $uploadToken;
if (!file_exists($path)) {
throw new Exception('Invalid upload token ' . $uploadToken, MIDAS_INVALID_UPLOAD_TOKEN);
}
@rmdir($path);
list($userId, $itemId) = explode('/', $uploadToken);
/** @var UserModel $userModel */
$userModel = MidasLoader::loadModel('User');
$userDao = $userModel->load($userId);
if ($userDao === false) {
throw new Exception('Invalid user id from upload token', MIDAS_INVALID_PARAMETER);
}
/** @var ItemModel $itemModel */
$itemModel = MidasLoader::loadModel('Item');
$itemDao = $itemModel->load($itemId);
if ($itemDao === false) {
throw new Exception('Unable to find item', MIDAS_INVALID_PARAMETER);
}
if (!$itemModel->policyCheck($itemDao, $userDao, MIDAS_POLICY_WRITE)) {
throw new Exception('Permission error', MIDAS_INVALID_POLICY);
}
if (array_key_exists('revision', $args)) {
if (strtolower($args['revision']) == 'head') {
$revision = $itemModel->getLastRevision($itemDao);
} else {
$revision = $itemModel->getRevision($itemDao, $args['revision']);
if ($revision == false) {
throw new Exception('Unable to find revision', MIDAS_INVALID_PARAMETER);
}
}
}
if (!array_key_exists('file', $args) || !array_key_exists('file', $_FILES)) {
throw new Exception('Parameter file is not defined', MIDAS_INVALID_PARAMETER);
}
$file = $_FILES['file'];
$name = $file['name'];
$tmpName = $file['tmp_name'];
$size = filesize($tmpName);
$folderDaos = $itemDao->getFolders();
/** @var FolderDao $folderDao */
$folderDao = $folderDaos[0];
$validations = Zend_Registry::get('notifier')->callback('CALLBACK_CORE_VALIDATE_UPLOAD', array('filename' => $name, 'size' => $size, 'path' => $tmpName, 'folderId' => $folderDao->getFolderId()));
foreach ($validations as $validation) {
if (!$validation['status']) {
throw new Exception($validation['message'], MIDAS_INVALID_POLICY);
}
}
$license = isset($args['license']) ? $args['license'] : null;
$checksum = md5_file($tmpName);
$revisionNumber = null;
if (isset($revision) && $revision !== false) {
$revisionNumber = $revision->getRevision();
}
if (isset($args['changes'])) {
$changes = $args['changes'];
} elseif ($revisionNumber === 1) {
$changes = 'Initial revision';
} else {
$changes = '';
}
move_uploaded_file($tmpName, $path);
/** @var UploadComponent $uploadComponent */
$uploadComponent = MidasLoader::loadComponent('Upload');
$itemDao = $uploadComponent->createNewRevision($userDao, $name, $path, $changes, $itemDao->getKey(), $revisionNumber, $license, $checksum, false, $size);
if ($itemDao === false) {
throw new Exception('Upload failed', MIDAS_INTERNAL_ERROR);
}
return $itemDao->toArray();
}
/**
* Extract a zip and returns the path where it was extracted.
*/
protected function _extractZip($bitstreamDao, $progressDao)
{
$dir = UtilityComponent::getTempDirectory() . '/archive_' . $bitstreamDao->getKey() . '_' . time();
if (!mkdir($dir)) {
throw new Zend_Exception('Could not write into temp directory');
}
$nativeCommand = $this->Setting->getValueByName(ARCHIVE_UNZIP_COMMAND_KEY, $this->moduleName);
if ($nativeCommand && $bitstreamDao->getSizebytes() > 1024 * 1024 * 1024) {
// Only use native exe on zips over 1GB
$this->_extractZipNative($bitstreamDao, $nativeCommand, $dir, $progressDao);
} else {
$this->_extractZipPhp($bitstreamDao, $dir, $progressDao);
}
return $dir;
}
/**
* Use thumbnailer to pre-process a bitstream to generate a jpeg file.
* Echoes an error message if a problem occurs (for the scheduler log).
*
* @param string $name name of the image to be pre-processed
* @param string $fullPath absolute path to the image to be pre-processed
* @return string
* @throws Zend_Exception
*/
public function preprocessByThumbnailer($name, $fullPath)
{
$tmpPath = UtilityComponent::getTempDirectory('thumbnailcreator');
if (!file_exists($tmpPath)) {
throw new Zend_Exception('Temporary thumbnail dir does not exist: ' . $tmpPath);
}
$copyDestination = $tmpPath . '/' . $name;
copy($fullPath, $copyDestination);
$jpegDestination = $tmpPath . '/' . $name . '.jpg';
/** @var RandomComponent $randomComponent */
$randomComponent = MidasLoader::loadComponent('Random');
while (file_exists($jpegDestination)) {
$jpegDestination = $tmpPath . '/' . $name . $randomComponent->generateInt() . '.jpg';
}
/** @var SettingModel $settingModel */
$settingModel = MidasLoader::loadModel('Setting');
$thumbnailerPath = $settingModel->getValueByName(MIDAS_THUMBNAILCREATOR_THUMBNAILER_KEY, $this->moduleName);
$thumbnailerParams = array($copyDestination, $jpegDestination);
$thumbnailerCmd = KWUtils::prepareExeccommand($thumbnailerPath, $thumbnailerParams);
if (KWUtils::isExecutable($thumbnailerPath)) {
KWUtils::exec($thumbnailerCmd);
} else {
unlink($copyDestination);
throw new Zend_Exception('Thumbnailer does not exist or you do not have execute permission. Please check the configuration of thumbnailcreator module.');
}
if (!file_exists($jpegDestination)) {
unlink($copyDestination);
throw new Zend_Exception('Problem executing thumbnailer on your system');
} else {
unlink($copyDestination);
return $jpegDestination;
}
}
/**
* Get the amount of data already uploaded.
*
* @param array $args
* @return array
* @throws Exception
*/
public function getOffset($args)
{
// check parameters
if (!array_key_exists($this->tokenParamName, $args)) {
throw new Exception('Parameter ' . $this->tokenParamName . ' is not defined', MIDAS_HTTPUPLOAD_PARAM_UNDEFINED);
}
$uploadToken = $args[$this->tokenParamName];
$offset = UtilityComponent::fileSize(UtilityComponent::getTempDirectory() . '/' . $uploadToken);
return array('offset' => $offset);
}
}
}
$items = $publicItems;
if (empty($items)) {
$errors .= oai_error('noRecordsMatch');
}
}
// break and clean up on error
if ($errors != '') {
oai_exit();
}
$output .= " <ListIdentifiers>\n";
// Will we need a ResumptionToken?
if (count($items) - $deliveredrecords > $MAXIDS) {
$token = get_token();
$tokensDir = UtilityComponent::getTempDirectory() . '/tokens';
if (!is_dir($tokensDir)) {
mkdir($tokensDir);
}
$tokensPath = $tokensDir . '/id-' . $token;
$fp = fopen($tokensPath, 'w');
$thendeliveredrecords = (int) $deliveredrecords + $MAXIDS;
fwrite($fp, "{$thendeliveredrecords}#");
fwrite($fp, "{$extquery}#");
fclose($fp);
$num_rows = count($items);
$restoken = ' <resumptionToken expirationDate="' . $expirationdatetime . '"
completeListSize="' . $num_rows . '"
cursor="' . $deliveredrecords . '">' . $token . "</resumptionToken>\n";
} elseif (isset($set_resumptionToken)) {
$num_rows = count($items);
/** Create default asset store. */
function createDefaultAssetstore()
{
Zend_Registry::set('models', array());
/** @var AssetstoreModel $assetStoreModel */
$assetStoreModel = MidasLoader::loadModel('Assetstore');
// path munging
require_once BASE_PATH . '/core/controllers/components/UtilityComponent.php';
$testAssetstoreBase = UtilityComponent::getTempDirectory() . '/test/';
$testAssetstoreBase = str_replace('tests/../', '', $testAssetstoreBase);
$testAssetstoreBase = str_replace('//', '/', $testAssetstoreBase);
// create assetstore directory
if (!is_dir($testAssetstoreBase)) {
mkdir($testAssetstoreBase);
}
$testAssetstore = $testAssetstoreBase . '/assetstore';
if (!is_dir($testAssetstore)) {
mkdir($testAssetstore);
}
// create default assetstore in db
require_once BASE_PATH . '/core/models/dao/AssetstoreDao.php';
$assetstoreDao = new AssetstoreDao();
$assetstoreDao->setName('Default');
$assetstoreDao->setPath($testAssetstore);
$assetstoreDao->setType(MIDAS_ASSETSTORE_LOCAL);
$assetStoreModel->save($assetstoreDao);
}
/** createParaviewPath */
public function createParaviewPath()
{
/** @var SettingModel $settingModel */
$settingModel = MidasLoader::loadModel('Setting');
$customTemporaryDirectory = $settingModel->getValueByName(VISUALIZE_TEMPORARY_DIRECTORY_KEY, $this->moduleName);
if (isset($customTemporaryDirectory) && !empty($customTemporaryDirectory)) {
$tmp_dir = $customTemporaryDirectory;
if (!file_exists($tmp_dir) || !is_writable($tmp_dir)) {
throw new Zend_Exception('Unable to access temp dir');
}
} else {
if (!file_exists(UtilityComponent::getTempDirectory() . '/visualize')) {
mkdir(UtilityComponent::getTempDirectory() . '/visualize');
}
$tmp_dir = UtilityComponent::getTempDirectory() . '/visualize';
}
$dir = opendir($tmp_dir);
while ($entry = readdir($dir)) {
if (is_dir($tmp_dir . '/' . $entry) && filemtime($tmp_dir . '/' . $entry) < strtotime('-1 hours') && !in_array($entry, array('.', '..'))) {
if (strpos($entry, 'Paraview') !== false) {
$this->_rrmdir($tmp_dir . '/' . $entry);
}
}
}
/** @var RandomComponent $randomComponent */
$randomComponent = MidasLoader::loadComponent('Random');
$tmpFolderName = 'ParaviewWeb_' . $randomComponent->generateInt();
$path = $tmp_dir . '/' . $tmpFolderName;
while (!mkdir($path)) {
$tmpFolderName = 'ParaviewWeb_' . $randomComponent->generateInt();
$path = $tmp_dir . '/' . $tmpFolderName;
}
return array('path' => $path, 'folderName' => $tmpFolderName);
}
/** tests recursiveRemoveDirectory function */
public function testRecursiveRemoveDirectory()
{
// test some basic exception handling
$this->assertFalse(KWUtils::recursiveRemoveDirectory(''));
$this->assertFalse(KWUtils::recursiveRemoveDirectory('thisstringisunlikelytobeadirectory'));
// create a two-level directory
$testParentDir = UtilityComponent::getTempDirectory() . '/KWUtilsParentDir';
mkdir($testParentDir);
$testChildDir = UtilityComponent::getTempDirectory() . '/KWUtilsParentDir/ChildDir';
mkdir($testChildDir);
copy(BASE_PATH . '/tests/testfiles/search.png', $testChildDir . '/testContent.png');
$this->assertTrue(file_exists($testChildDir . '/testContent.png'));
// recursively remove the directory
KWUtils::recursiveRemoveDirectory($testParentDir);
$this->assertFalse(file_exists($testParentDir));
}
/**
* Handle the get dashboard callback.
*
* @return array map of dashboard fields to their values
*/
public function getDasboard()
{
return array('Data Folder Writable' => array(is_writable(UtilityComponent::getDataDirectory())), 'Temporary Folder Writable' => array(is_writable(UtilityComponent::getTempDirectory(''))));
}