/**
* exec method with the same interface as that in KWUtils, will check the
* command and intercept it if it is a known command with a Mock object
* that should be used for testing, otherwise it will pass it on to KWUtils.
*
* @param type $command
* @param type $output
* @param type $chdir
* @param type $return_val
*/
public function exec($command, &$output = null, $chdir = '', &$return_val = null)
{
$matched = false;
foreach ($this->mockExes as $exeName => $mockExe) {
if (preg_match('/' . $exeName . '/', $command)) {
$matched = true;
$mockExe->exec($command, $output, $chdir, $return_val);
}
}
if (!$matched) {
KWUtils::exec($command, $output, $chdir, $return_val);
}
}
/**
* function will create a temporary batchmake config, copying over test data
* to the the locations in that config needed for the tests, returning an
* array of config property names to directory locations.
*
* @todo figure out a way to copy over Batchmake or else mock it
* @return array
* @throws Zend_Exception
*/
public function setupAndGetConfig()
{
// create a test batchmake setup in the temp dir
// and initialize test data
$tmpDir = $this->getTempDirectory();
$subDirs = array('batchmake', 'tests');
KWUtils::createSubDirectories($tmpDir . '/', $subDirs);
$configProps = array(MIDAS_BATCHMAKE_TMP_DIR_PROPERTY => $tmpDir . '/batchmake/tests/tmp', MIDAS_BATCHMAKE_BIN_DIR_PROPERTY => $tmpDir . '/batchmake/tests/bin', MIDAS_BATCHMAKE_SCRIPT_DIR_PROPERTY => $tmpDir . '/batchmake/tests/script', MIDAS_BATCHMAKE_APP_DIR_PROPERTY => $tmpDir . '/batchmake/tests/bin', MIDAS_BATCHMAKE_DATA_DIR_PROPERTY => $tmpDir . '/batchmake/tests/data', MIDAS_BATCHMAKE_CONDOR_BIN_DIR_PROPERTY => $tmpDir . '/batchmake/tests/condorbin');
// now make sure these dirs exist
// later can actually add some stuff to these dirs
foreach ($configProps as $dir) {
if (!file_exists($dir) && !KWUtils::mkDir($dir)) {
throw new Zend_Exception("couldn't create dir " . $dir);
}
}
// now copy over the bms files
$srcDir = BASE_PATH . 'modules/batchmake/tests/testfiles/script';
$targetDir = $configProps[MIDAS_BATCHMAKE_SCRIPT_DIR_PROPERTY];
$extension = '.bms';
$this->symlinkFileset($srcDir, $targetDir, $extension);
// and now the bmms
$srcDir = BASE_PATH . 'modules/batchmake/tests/testfiles/bin';
$targetDir = $configProps[MIDAS_BATCHMAKE_APP_DIR_PROPERTY];
$extension = '.bmm';
$this->symlinkFileset($srcDir, $targetDir, $extension);
// the mock object strategy requires both an interface and for
// executable files to exist on disk in a particular location,
// so here we will create symlinks to a known executable
// ls
// which should be on most systems
$params = array('ls');
$cmd = KWUtils::prepareExeccommand('which', $params);
// dir doesn't matter, just send in srcDir as it is convenient
KWUtils::exec($cmd, $output, $srcDir, $returnVal);
if ($returnVal !== 0 || !isset($output) || !isset($output[0])) {
throw new Zend_Exception('Problem finding ls on your system, used for testing');
}
$pathToLs = $output[0];
// get the applications and their path properties from the component that
// expects them
$applicationsPaths = Batchmake_KWBatchmakeComponent::getApplicationsPaths();
foreach ($applicationsPaths as $application => $pathProperty) {
// now in the place of each executable, symlink the ls exe
$link = $configProps[$pathProperty] . '/' . $application;
if (!file_exists($link) && !symlink($pathToLs, $link)) {
throw new Zend_Exception($pathToLs . ' could not be sym-linked to ' . $link);
}
}
return $configProps;
}
/**
* Stop DICOM server.
*
* @path /dicomserver/server/stop
* @http POST
* @param storescp_cmd (Optional) The command to run storescp
* @param dcmqrscp_cmd (Optional) The command to run dcmqrscp
* @param incoming_dir (Optional) The incoming directory to receive and process DICOM files
* @param get_command (Optional) If set, will not stop DICOM server, but only get command used to stop DICOM server in command line.
* @return
*/
public function stop($args)
{
// Only administrator can call this api
$userDao = Zend_Registry::get('userSession')->Dao;
if (!$userDao || !$userDao->isAdmin()) {
throw new Exception('Only administrator can stop DICOM server', MIDAS_INVALID_POLICY);
}
$ret = array();
$status_args = array();
if (!empty($args['storescp_cmd'])) {
$status_args['storescp_cmd'] = $args['storescp_cmd'];
}
if (!empty($args['dcmqrscp_cmd'])) {
$status_args['dcmqrscp_cmd'] = $args['dcmqrscp_cmd'];
}
$running_status = $this->status($status_args);
if ($running_status['status'] == MIDAS_DICOMSERVER_SERVER_NOT_RUNNING && !array_key_exists('get_command', $args)) {
$ret['message'] = 'DICOM server is not running now!';
return $ret;
}
$storescp_cmd = 'storescp';
if (!empty($args['storescp_cmd'])) {
$storescp_cmd = $args['storescp_cmd'];
}
$dcmqrscp_cmd = 'dcmqrscp';
if (!empty($args['dcmqrscp_cmd'])) {
$dcmqrscp_cmd = $args['dcmqrscp_cmd'];
}
if (!empty($args['incoming_dir'])) {
$incoming_dir = $args['incoming_dir'];
} else {
/** @var Dicomserver_ServerComponent $serverComponent */
$serverComponent = MidasLoader::loadComponent('Server', 'dicomserver');
$incoming_dir = $serverComponent->getDefaultReceptionDir();
}
$log_dir = $incoming_dir . MIDAS_DICOMSERVER_LOGS_DIRECTORY;
if (!file_exists($log_dir)) {
KWUtils::mkDir($log_dir, 0777);
}
$python_cmd = 'python';
$python_params = array();
$python_params[] = BASE_PATH . '/modules/dicomserver/library/serverWrapper.py';
$python_params[] = '--stop';
$python_params[] = '-i ' . $incoming_dir;
$python_params[] = '-s ' . $storescp_cmd;
$python_params[] = '-q ' . $dcmqrscp_cmd;
$stop_server_command = KWUtils::prepareExeccommand($python_cmd, $python_params);
if (array_key_exists('get_command', $args)) {
$stop_server_command_string = str_replace("'", '', $stop_server_command);
return escapeshellarg($stop_server_command_string);
}
KWUtils::exec($stop_server_command, $output, '', $returnVal);
$ret['message'] = 'Succeeded to stop DICOM C-STORE receiver and Query-Retrieve services!';
if ($returnVal) {
$exception_string = "Failed to stop DICOM server! \n Reason:" . implode("\n", $output);
throw new Zend_Exception(htmlspecialchars($exception_string, ENT_QUOTES), MIDAS_INVALID_POLICY);
}
return $ret;
}
/**
* 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 $jpegDestination;
}
}
/**
* Register DICOM image files (bitstreams).
*/
public function register($revision)
{
$bitstreams = $revision->getBitstreams();
if (count($bitstreams) < 1) {
return;
}
/** @var SettingModel $settingModel */
$settingModel = MidasLoader::loadModel('Setting');
$command = $settingModel->getValueByName(MIDAS_DICOMSERVER_DCMQRIDX_COMMAND_KEY, $this->moduleName);
$command = str_replace("'", '', $command);
$commandParams = array();
$receptionDirectory = $settingModel->getValueByName(MIDAS_DICOMSERVER_RECEPTION_DIRECTORY_KEY, $this->moduleName);
if (!is_writable($receptionDirectory)) {
throw new Zend_Exception('Please configure Dicom Server module correctly. Its reception directory is NOT writable!', MIDAS_INVALID_POLICY);
}
$aeStorage = $receptionDirectory . MIDAS_DICOMSERVER_PACS_DIRECTORY;
$aeStorage = str_replace("'", '', $aeStorage);
$commandParams[] = $aeStorage;
foreach ($bitstreams as $bitstream) {
$commandParams[] = $bitstream->getFullPath();
$registerCommand = KWUtils::prepareExeccommand($command, $commandParams);
array_pop($command_params);
// prepare for next iteration in the loop
KWUtils::exec($registerCommand, $output, '', $returnVal);
if ($returnVal) {
$exceptionString = "Failed to register DICOM images! \n Reason:" . implode("\n", $output);
throw new Zend_Exception(htmlspecialchars($exceptionString, ENT_QUOTES), MIDAS_INVALID_POLICY);
}
}
/** @var Dicomserver_RegistrationModel $registrationModel */
$registrationModel = MidasLoader::loadModel('Registration', 'dicomserver');
$itemId = $revision->getItemId();
if (!$registrationModel->checkByItemId($itemId)) {
$registrationModel->createRegistration($itemId);
}
}
/** tests exec function */
public function testExec()
{
// Do not run this on Windows until can figure out how to test it
if (KWUtils::isWindows()) {
return;
}
// not sure how to test this exactly, for now create a tmp dir, check
// the value of pwd in it
$initialCwd = getcwd();
$output = null;
$returnVal = null;
// create a tmp dir for this test
$execDir = UtilityComponent::getTempDirectory() . '/KWUtilsTest';
mkdir($execDir);
$cmd = 'pwd';
$chdir = $execDir;
KWUtils::exec($cmd, $output, $chdir, $returnVal);
// $output should have one value, the same as execDir
$postCwd = getcwd();
// check that we are back to the original directory after the exec
// we are already checking with this test that we chdir correctly because
// the test changes into a dir and then performs pwd there
$this->assertEquals($initialCwd, $postCwd, "exec didn't correctly return to the origin directory");
// yuck, need to do a bit of munging to get around tests/.. in BASE_PATH
$execDir = str_replace('tests/../', '', $execDir);
// and now replace any // with /,
// the // doesn't affect functionality on the
// filesystem, but will cause string inequality
$execDir = str_replace('//', '/', $execDir);
$this->assertEquals($execDir, $output[0]);
// returnVal should be 0
$this->assertEquals($returnVal, 0);
// now clean up the tmp dir
rmdir($execDir);
// pass in a bad cwd, be sure that we get an exception
$chdir = '/this/dir/probably/will/not/exist/anywhere';
$output = null;
$returnVal = null;
try {
KWUtils::exec($cmd, $output, $chdir, $returnVal);
$this->fail();
} catch (Zend_Exception $ze) {
// this is the correct behavior
$this->assertTrue(true);
}
$postCwd = getcwd();
// ensure we are still in the same directory
$this->assertEquals($initialCwd, $postCwd, "exec didn't correctly return to the origin directory");
// now try to run pwd passing in a null chdir
// should return an output the same as the initialCwd
$chdir = null;
$output = null;
$returnVal = null;
KWUtils::exec($cmd, $output, $chdir, $returnVal);
// ensure that it ran in the initialCwd
$this->assertEquals($initialCwd, $output[0]);
// check that we are still in the output dir
$postCwd = getcwd();
$this->assertEquals($initialCwd, $postCwd);
}
/**
* forwards a call to this method on to KWUtils.exec, with the same
* method signature.
*
* @param string $command
* @param null|mixed $output
* @param string $chdir
* @param null|mixed $return_val
* @throws Zend_Exception
*/
public function exec($command, &$output = null, $chdir = '', &$return_val = null)
{
KWUtils::exec($command, $output, $chdir, $return_val);
}
