delete_tus_file() - Code Metrics - Inspection of "1.3.0" - salimkanoun/GaelO - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Pull Request — master (#103)

by Salim

created 2020-10-28 21:36 UTC

delete_tus_file() A

↳ Parent: Project

Complexity

Conditions	1
Paths	1

Size

Total Lines	9
Code Lines	4

Duplication

Lines	0
Ratio	0 %

Importance

Changes	1
Bugs	0	Features	0

Metric	Value
cc	1
eloc	4
nc	1
nop	1
dl	0
loc	9
rs	10
c	1
b	0
f	0

<?php
/**
 Copyright (C) 2018-2020 KANOUN Salim
 This program is free software; you can redistribute it and/or modify
 it under the terms of the Affero GNU General Public v.3 License as published by
 the Free Software Foundation;
 This program is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 Affero GNU General Public Public for more details.
 You should have received a copy of the Affero GNU General Public Public along
 with this program; if not, write to the Free Software Foundation, Inc.,
 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
 */

/**
 * Validate the uploaded dicom, this script act as follow : 
 * Unzip the recieved ZIPs
 * Send each dicom to Orthanc Exposed
 * Produce the Anonymize query in Orthanc Exposed
 * Delete the original import in Orthanc Exposed
 * Send the anonymized study in Orthanc PACS
 * Delete the anonymied dicom in Orthanc Exposed
 * Analyze the Orthanc PACS dicom and write DICOM details in database
 * Update Visit status and send email notifications
 * 
 * Warning : The execution time of this script is long due to Orthanc heavy operations
 * Double check the timeout value that are set in Orthanc class and that database connexion is not timed up
 * Check also the max execution time (which is reset in Orthanc class)
 * 
 */

require_once($_SERVER['DOCUMENT_ROOT'].'/vendor/autoload.php');

use GuzzleHttp\Client;
filter:
    dependency_paths: ["lib/*"]

Session::checkSession();
$linkpdo=Session::getLinkpdo();

$timeStamp = $_POST['timeStamp'];
$id_visit = $_POST['id_visit'];
$nbOfInstances = $_POST['totalDicomFiles'];
$anonFromOrthancId=$_POST['originalOrthancStudyID'];
$username=$_SESSION['username'];
$study=$_SESSION['study'];
$role=$_SESSION['role'];
$tusFilesID = json_decode($_POST['sucessIDsUploaded']);

$unzipedPath = $_SERVER['DOCUMENT_ROOT'].'/data/upload/temp/'.$timeStamp.'_'.$id_visit;

$visitObject=new Visit($id_visit, $linkpdo);
$userObject=new User($username, $linkpdo);

$accessCheck=$userObject->isVisitAllowed($id_visit, User::INVESTIGATOR);

if ($accessCheck && $role == User::INVESTIGATOR && $visitObject->uploadStatus == Visit::NOT_DONE) {
	
	//Run as a background task even if the user leave the website
	ignore_user_abort(true);
	//Set Visit as upload processing status
	$visitObject->changeUploadStatus(Visit::UPLOAD_PROCESSING);
    $start_time=microtime(true);
	/**
	 * Try block as each interruption of the proccess must make visit return as upload not done
	 * To allow new upload
	 */
	try {

		if (!is_dir($unzipedPath)) {
			mkdir($unzipedPath, 0755);
		}

		//Unzip each uploaded file and remove them from tus
		foreach($tusFilesID as $fileName){
			$tempZipPath = get_tus_file($fileName);

			$zipSize=filesize($tempZipPath);
			$uncompressedzipSize=get_zip_originalsize($tempZipPath);
			if ($uncompressedzipSize/$zipSize > 50) {
				throw new Exception("Bomb Zip");
			}

			$zip=new ZipArchive;
			$zip->open($tempZipPath);
			$zip->extractTo($unzipedPath);
			$zip->close();
			
			//Remove file from TUS and downloaded temporary zip
			delete_tus_file($fileName);
			unlink($tempZipPath);

		}
		


		//Send unziped files to Orthanc
		$orthancExposedObject=new Orthanc(true);
		$importedMap=sendFolderToOrthanc($unzipedPath, $orthancExposedObject);
class A
{
    function getObject()
    {
        return null;
    }

}

$a = new A();
$object = $a->getObject();

		//Anonymize, remove original and send anonymized to Orthanc PACS
		//Read imported map, it only have only one study
		foreach ($importedMap as $studyID=>$seriesIDs) {

			//Anonymize and store new anonymized study Orthanc ID
			$anonymizedIDArray[]=$orthancExposedObject->Anonymize($studyID, $visitObject->getVisitCharacteristics()->anonProfile, $visitObject->patientCode, $visitObject->visitType, $visitObject->study);
			//error_log("Anonymization done at ".(microtime(true)-$start_time));
			//Delete original import
			$orthancExposedObject->deleteFromOrthanc("studies", $studyID);
			
		}
		//Send to Orthanc Pacs and fill the database
		$orthancExposedObject->sendToPeer("OrthancPacs", $anonymizedIDArray);
		//error_log("Peer sent at ".(microtime(true)-$start_time));
		//erase transfered anonymized study from orthanc exposed
		$orthancExposedObject->deleteFromOrthanc("studies", $anonymizedIDArray[0]);
	
		//Fill the Orthanc study / series table
		//Reset the PDO object as the database connexion is likely to be timed out
		$linkpdo=Session::getLinkpdo();
		$fillTable=new Fill_Orthanc_Table($visitObject->id_visit, $username, $linkpdo);
		$studyDetails=$fillTable->parseData($anonymizedIDArray[0]);

		//Check that nb on instances in Orthanc PACS still match the original number of sent instances
		if ($studyDetails['countInstances'] != $nbOfInstances) {
			throw new Exception("Error during Peer transfers"); 
		}
    		
		//Fill Orthanc Tables in Database and update visit status
		$fillTable->fillDB($anonFromOrthancId);
		$answer['receivedConfirmation']=true;
		$logDetails['uploadedSeries']=$studyDetails['seriesInStudy'];
		$logDetails['patientNumber']=$visitObject->patientCode;
		$logDetails['visitType']=$visitObject->visitType;
		$logDetails['modality_visit']=$visitObject->visitGroupObject->groupModality;
		//Log import
		Tracker::logActivity($username, $role, $study, $visitObject->id_visit, "Upload Series", $logDetails);
	
	}catch (Throwable $e1) {
		error_log($e1->getMessage());
		handleException($e1);
	}
		

}else {
	header('HTTP/1.0 403 Forbidden');
	die('You are not allowed to access this file.');
}


/**
 * Send all folder content to Orthanc (recursively)
 * @param string $unzipedPath
 * @param Orthanc $orthancExposedObject
 * @throws Exception
 * @return mixed
 */
function sendFolderToOrthanc(string $unzipedPath, Orthanc $orthancExposedObject) {
	
	global $nbOfInstances;
	//Recursive scann of the unzipped folder
	$rii=new RecursiveIteratorIterator(new RecursiveDirectoryIterator($unzipedPath));
	
	$files=array();
	foreach ($rii as $file) {
		if ($file->isDir()) {
			continue;
		}
		$files[]=$file->getPathname();
    }
    
    if(sizeof($files) != $nbOfInstances){
        throw new Exception("Number Of Uploaded Files dosen't match expected instance number");
    }
	
	$importedMap=null;
	$importedInstances=0;
	//$start_time=microtime(true);
	
	//Import dicom file one by one
	foreach ($files as $file) {
		$importAnswer=$orthancExposedObject->importFile($file);
		if (!empty($importAnswer)) {
			$answerdetails=json_decode($importAnswer, true);
			$importedMap[$answerdetails['ParentStudy']][$answerdetails['ParentSeries']][]=$answerdetails['ID'];
			$importedInstances++;
		}
		
	}
	
	//Delete original file after import
	recursive_directory_delete($unzipedPath);
	
	//error_log("Imported ".$importedInstances." files in ".(microtime(true)-$start_time));
	error_log('Imported Instances :'.$importedInstances);
	error_log('Announced number of Instances :'.$nbOfInstances);
	
	if (count($importedMap) == 1 && $importedInstances == $nbOfInstances) {
		return $importedMap;
	}else {
		//These error shall never occur
		if (count($importedMap) > 1) {
			throw new Exception("More than one study in Zip");
		}else if ($importedInstances != $nbOfInstances) {
			throw new Exception("Imported DICOM not matching announced number of Instances");
			
		}
	}
	
}

/**
 * Recursively delete unziped folder
 * @param string $directory
 */
function recursive_directory_delete(string $directory) {
	$it=new RecursiveDirectoryIterator($directory, FilesystemIterator::SKIP_DOTS);
	$it=new RecursiveIteratorIterator($it, RecursiveIteratorIterator::CHILD_FIRST);
	foreach ($it as $file) {
		if ($file->isDir()) rmdir($file->getPathname());
		else unlink($file->getPathname());
	}
	rmdir($directory);
}

/**
 * In case of a thrown exception, warn administrator and uploader and set upload to not done
 * @param Exception $e1
 */
function handleException(Throwable $e1) {
	global $visitObject;
	global $linkpdo;
	global $answer;
	//If more than own study uploaded or difference of instance number an exception is thrown
	$answer['receivedConfirmation']=false;
	$answer['errorDetails']=$e1->getMessage();
	$visitObject->changeUploadStatus(Visit::NOT_DONE);
	warningAdminError($e1->getMessage(), $linkpdo);
	die($e1->getMessage());

}
/**
 * Warn supervisors and uploader that validation of uploaded DICOM has failed
 * @param string $errorMessage
 * @param PDO $linkpdo
 */
function warningAdminError(string $errorMessage, PDO $linkpdo) {
	$sendEmails=new Send_Email($linkpdo);
	global $visitObject;
	global $unzipedPath;
	global $study;
	global $username;

	$sendEmails->addGroupEmails($study, User::SUPERVISOR)->addEmail($sendEmails->getUserEmails($username));
	$sendEmails->sendUploadValidationFailure($visitObject->id_visit, $visitObject->patientCode, $visitObject->visitType,
			$study, $unzipedPath, $username, $errorMessage);
}

/**
 * Get uncompressed Size
 * @param string $filename
 * @return number
 */
function get_zip_originalsize(string $filename) {
	$size=0;
	$resource=zip_open($filename);
	while ($dir_resource=zip_read($resource)) {
		$size+=zip_entry_filesize($dir_resource);
	}
	zip_close($resource);
    
	return $size;
}

function get_tus_file($fileName) {
    
    $client = new Client([
        // Base URI is used with relative requests
		'base_uri' => TUS_SERVER.'/tus/',
		'headers' => ['Tus-Resumable' => '1.0.0']
    ]);
	$downloadedFileName = tempnam(sys_get_temp_dir(), 'dicom');

	$resource  = fopen( $downloadedFileName, 'r+');
	
	$client->request('GET', $fileName, ['sink' => $resource]);

    return $downloadedFileName;
}

function delete_tus_file($fileName){

    $client = new Client([
        // Base URI is used with relative requests
		'base_uri' => TUS_SERVER.'/tus/',
		'headers' => ['Tus-Resumable' => '1.0.0']
    ]);

	$client->request('DELETE', $fileName);
	
    //$code = $response->getStatusCode(); // 200
	//$reason = $response->getReasonPhrase(); // OK

}





1			<?php
2			/**
3			Copyright (C) 2018-2020 KANOUN Salim
4			This program is free software; you can redistribute it and/or modify
5			it under the terms of the Affero GNU General Public v.3 License as published by
6			the Free Software Foundation;
7			This program is distributed in the hope that it will be useful,
8			but WITHOUT ANY WARRANTY; without even the implied warranty of
9			MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
10			Affero GNU General Public Public for more details.
11			You should have received a copy of the Affero GNU General Public Public along
12			with this program; if not, write to the Free Software Foundation, Inc.,
13			51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
14			*/
15
16			/**
17			* Validate the uploaded dicom, this script act as follow :
18			* Unzip the recieved ZIPs
19			* Send each dicom to Orthanc Exposed
20			* Produce the Anonymize query in Orthanc Exposed
21			* Delete the original import in Orthanc Exposed
22			* Send the anonymized study in Orthanc PACS
23			* Delete the anonymied dicom in Orthanc Exposed
24			* Analyze the Orthanc PACS dicom and write DICOM details in database
25			* Update Visit status and send email notifications
26			*
27			* Warning : The execution time of this script is long due to Orthanc heavy operations
28			* Double check the timeout value that are set in Orthanc class and that database connexion is not timed up
29			* Check also the max execution time (which is reset in Orthanc class)
30			*
31			*/
32
33			require_once($_SERVER['DOCUMENT_ROOT'].'/vendor/autoload.php');
34
35			use GuzzleHttp\Client;
			0 ignored issues – show Bug introduced 2020-08-09 15:15 UTC by Report Bug Copy Issue Report The type `GuzzleHttp\Client` was not found. Maybe you did not declare it correctly or list all dependencies? The issue could also be caused by a filter entry in the build configuration. If the path has been excluded in your configuration, e.g. `excluded_paths: ["lib/"]`, you can move it to the dependency path list as follows: filter: dependency_paths: ["lib/"] For further information see https://scrutinizer-ci.com/docs/tools/php/php-scrutinizer/#list-dependency-paths Loading history...
36
37			Session::checkSession();
38			$linkpdo=Session::getLinkpdo();
39
40			$timeStamp = $_POST['timeStamp'];
41			$id_visit = $_POST['id_visit'];
42			$nbOfInstances = $_POST['totalDicomFiles'];
43			$anonFromOrthancId=$_POST['originalOrthancStudyID'];
44			$username=$_SESSION['username'];
45			$study=$_SESSION['study'];
46			$role=$_SESSION['role'];
47			$tusFilesID = json_decode($_POST['sucessIDsUploaded']);
48
49			$unzipedPath = $_SERVER['DOCUMENT_ROOT'].'/data/upload/temp/'.$timeStamp.'_'.$id_visit;
50
51			$visitObject=new Visit($id_visit, $linkpdo);
52			$userObject=new User($username, $linkpdo);
53
54			$accessCheck=$userObject->isVisitAllowed($id_visit, User::INVESTIGATOR);
55
56			if ($accessCheck && $role == User::INVESTIGATOR && $visitObject->uploadStatus == Visit::NOT_DONE) {
57
58			//Run as a background task even if the user leave the website
59			ignore_user_abort(true);
60			//Set Visit as upload processing status
61			$visitObject->changeUploadStatus(Visit::UPLOAD_PROCESSING);
62			$start_time=microtime(true);
63			/**
64			* Try block as each interruption of the proccess must make visit return as upload not done
65			* To allow new upload
66			*/
67			try {
68
69			if (!is_dir($unzipedPath)) {
70			mkdir($unzipedPath, 0755);
71			}
72
73			//Unzip each uploaded file and remove them from tus
74			foreach($tusFilesID as $fileName){
75			$tempZipPath = get_tus_file($fileName);
76
77			$zipSize=filesize($tempZipPath);
78			$uncompressedzipSize=get_zip_originalsize($tempZipPath);
79			if ($uncompressedzipSize/$zipSize > 50) {
80			throw new Exception("Bomb Zip");
81			}
82
83			$zip=new ZipArchive;
84			$zip->open($tempZipPath);
85			$zip->extractTo($unzipedPath);
86			$zip->close();
87
88			//Remove file from TUS and downloaded temporary zip
89			delete_tus_file($fileName);
90			unlink($tempZipPath);
91
92			}
93
94
95
96			//Send unziped files to Orthanc
97			$orthancExposedObject=new Orthanc(true);
98			$importedMap=sendFolderToOrthanc($unzipedPath, $orthancExposedObject);
			0 ignored issues – show Bug introduced 2020-07-29 23:10 UTC by Report Bug Copy Issue Report Are you sure the assignment to `$importedMap` is correct as `sendFolderToOrthanc($unz... $orthancExposedObject)` seems to always return `null`. This check looks for function or method calls that always return null and whose return value is assigned to a variable. class A { function getObject() { return null; } } $a = new A(); $object = $a->getObject(); The method `getObject()` can return nothing but null, so it makes no sense to assign that value to a variable. The reason is most likely that a function or method is imcomplete or has been reduced for debug purposes. Loading history...
99
100			//Anonymize, remove original and send anonymized to Orthanc PACS
101			//Read imported map, it only have only one study
102			foreach ($importedMap as $studyID=>$seriesIDs) {
			0 ignored issues – show Bug introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report The expression `$importedMap` of type `null` is not traversable. Loading history...
103			//Anonymize and store new anonymized study Orthanc ID
104			$anonymizedIDArray[]=$orthancExposedObject->Anonymize($studyID, $visitObject->getVisitCharacteristics()->anonProfile, $visitObject->patientCode, $visitObject->visitType, $visitObject->study);
105			//error_log("Anonymization done at ".(microtime(true)-$start_time));
106			//Delete original import
107			$orthancExposedObject->deleteFromOrthanc("studies", $studyID);
108
109			}
110			//Send to Orthanc Pacs and fill the database
111			$orthancExposedObject->sendToPeer("OrthancPacs", $anonymizedIDArray);
112			//error_log("Peer sent at ".(microtime(true)-$start_time));
113			//erase transfered anonymized study from orthanc exposed
114			$orthancExposedObject->deleteFromOrthanc("studies", $anonymizedIDArray[0]);
115
116			//Fill the Orthanc study / series table
117			//Reset the PDO object as the database connexion is likely to be timed out
118			$linkpdo=Session::getLinkpdo();
119			$fillTable=new Fill_Orthanc_Table($visitObject->id_visit, $username, $linkpdo);
120			$studyDetails=$fillTable->parseData($anonymizedIDArray[0]);
121
122			//Check that nb on instances in Orthanc PACS still match the original number of sent instances
123			if ($studyDetails['countInstances'] != $nbOfInstances) {
124			throw new Exception("Error during Peer transfers");
125			}
126
127			//Fill Orthanc Tables in Database and update visit status
128			$fillTable->fillDB($anonFromOrthancId);
129			$answer['receivedConfirmation']=true;
130			$logDetails['uploadedSeries']=$studyDetails['seriesInStudy'];
131			$logDetails['patientNumber']=$visitObject->patientCode;
132			$logDetails['visitType']=$visitObject->visitType;
133			$logDetails['modality_visit']=$visitObject->visitGroupObject->groupModality;
134			//Log import
135			Tracker::logActivity($username, $role, $study, $visitObject->id_visit, "Upload Series", $logDetails);
136
137			}catch (Throwable $e1) {
138			error_log($e1->getMessage());
139			handleException($e1);
140			}
141
142
143			}else {
144			header('HTTP/1.0 403 Forbidden');
145			die('You are not allowed to access this file.');
146			}
147
148
149			/**
150			* Send all folder content to Orthanc (recursively)
151			* @param string $unzipedPath
152			* @param Orthanc $orthancExposedObject
153			* @throws Exception
154			* @return mixed
155			*/
156			function sendFolderToOrthanc(string $unzipedPath, Orthanc $orthancExposedObject) {
157
158			global $nbOfInstances;
159			//Recursive scann of the unzipped folder
160			$rii=new RecursiveIteratorIterator(new RecursiveDirectoryIterator($unzipedPath));
161
162			$files=array();
163			foreach ($rii as $file) {
164			if ($file->isDir()) {
165			continue;
166			}
167			$files[]=$file->getPathname();
168			}
169
170			if(sizeof($files) != $nbOfInstances){
171			throw new Exception("Number Of Uploaded Files dosen't match expected instance number");
172			}
173
174			$importedMap=null;
175			$importedInstances=0;
176			//$start_time=microtime(true);
177
178			//Import dicom file one by one
179			foreach ($files as $file) {
180			$importAnswer=$orthancExposedObject->importFile($file);
181			if (!empty($importAnswer)) {
182			$answerdetails=json_decode($importAnswer, true);
183			$importedMap[$answerdetails['ParentStudy']][$answerdetails['ParentSeries']][]=$answerdetails['ID'];
184			$importedInstances++;
185			}
186
187			}
188
189			//Delete original file after import
190			recursive_directory_delete($unzipedPath);
191
192			//error_log("Imported ".$importedInstances." files in ".(microtime(true)-$start_time));
193			error_log('Imported Instances :'.$importedInstances);
194			error_log('Announced number of Instances :'.$nbOfInstances);
195
196			if (count($importedMap) == 1 && $importedInstances == $nbOfInstances) {
197			return $importedMap;
198			}else {
199			//These error shall never occur
200			if (count($importedMap) > 1) {
201			throw new Exception("More than one study in Zip");
202			}else if ($importedInstances != $nbOfInstances) {
203			throw new Exception("Imported DICOM not matching announced number of Instances");
204
205			}
206			}
207
208			}
209
210			/**
211			* Recursively delete unziped folder
212			* @param string $directory
213			*/
214			function recursive_directory_delete(string $directory) {
215			$it=new RecursiveDirectoryIterator($directory, FilesystemIterator::SKIP_DOTS);
216			$it=new RecursiveIteratorIterator($it, RecursiveIteratorIterator::CHILD_FIRST);
217			foreach ($it as $file) {
218			if ($file->isDir()) rmdir($file->getPathname());
219			else unlink($file->getPathname());
220			}
221			rmdir($directory);
222			}
223
224			/**
225			* In case of a thrown exception, warn administrator and uploader and set upload to not done
226			* @param Exception $e1
227			*/
228			function handleException(Throwable $e1) {
229			global $visitObject;
230			global $linkpdo;
231			global $answer;
232			//If more than own study uploaded or difference of instance number an exception is thrown
233			$answer['receivedConfirmation']=false;
234			$answer['errorDetails']=$e1->getMessage();
235			$visitObject->changeUploadStatus(Visit::NOT_DONE);
236			warningAdminError($e1->getMessage(), $linkpdo);
237			die($e1->getMessage());
			0 ignored issues – show Best Practice introduced 2020-07-29 23:10 UTC by Report Bug Copy Issue Report Using `exit` here is not recommended. In general, usage of exit should be done with care and only when running in a scripting context like a CLI script. Loading history...
238			}
239			/**
240			* Warn supervisors and uploader that validation of uploaded DICOM has failed
241			* @param string $errorMessage
242			* @param PDO $linkpdo
243			*/
244			function warningAdminError(string $errorMessage, PDO $linkpdo) {
245			$sendEmails=new Send_Email($linkpdo);
246			global $visitObject;
247			global $unzipedPath;
248			global $study;
249			global $username;
250
251			$sendEmails->addGroupEmails($study, User::SUPERVISOR)->addEmail($sendEmails->getUserEmails($username));
252			$sendEmails->sendUploadValidationFailure($visitObject->id_visit, $visitObject->patientCode, $visitObject->visitType,
253			$study, $unzipedPath, $username, $errorMessage);
254			}
255
256			/**
257			* Get uncompressed Size
258			* @param string $filename
259			* @return number
260			*/
261			function get_zip_originalsize(string $filename) {
262			$size=0;
263			$resource=zip_open($filename);
264			while ($dir_resource=zip_read($resource)) {
265			$size+=zip_entry_filesize($dir_resource);
266			}
267			zip_close($resource);
268
269			return $size;
270			}
271
272			function get_tus_file($fileName) {
273
274			$client = new Client([
275			// Base URI is used with relative requests
276			'base_uri' => TUS_SERVER.'/tus/',
277			'headers' => ['Tus-Resumable' => '1.0.0']
278			]);
279			$downloadedFileName = tempnam(sys_get_temp_dir(), 'dicom');
280
281			$resource = fopen( $downloadedFileName, 'r+');
282
283			$client->request('GET', $fileName, ['sink' => $resource]);
284
285			return $downloadedFileName;
286			}
287
288			function delete_tus_file($fileName){
289
290			$client = new Client([
291			// Base URI is used with relative requests
292			'base_uri' => TUS_SERVER.'/tus/',
293			'headers' => ['Tus-Resumable' => '1.0.0']
294			]);
295
296			$client->request('DELETE', $fileName);
297
298			//$code = $response->getStatusCode(); // 200
299			//$reason = $response->getReasonPhrase(); // OK
300
301			}
302
303
304
305

salimkanoun / GaelO

Pull Request — master (#103)

delete_tus_file() A

Complexity

Size

Duplication

Importance

Duplication Side-by-Side

Filter issues like